bluuebunny/crossref_metadata_2025_split huggingface dataset:
grenedalf: population genetic statistics for the next generation of pool sequencing
Authors: Czech Lucas , Spence Jeffrey P , Expósito-Alonso Moisés 
Published: August 2024

Abstract

Summary
Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written in C++ that implements common population genetic statistics such as θ, Tajima’s D, and FST for Pool sequencing. It is orders of magnitude faster than current tools, and is focused on providing usability and scalability, while also offering a plethora of input file formats and convenience options.

Availability and implementation
grenedalf is published under the GPL-3, and freely available at github.com/lczech/grenedalf.
Lichen planus following COVID-19 vaccination: a narrative review
Authors: D’Agostino Michela , Martora Fabrizio , Megna Matteo , Napolitano Maddalena , Potestio Luca 
Published: August 2024

Abstract
Lichen planus (LP) is an inflammatory disease that afflicts the skin, mucous membranes and cutaneous appendages. Moreover, LP represents a prototype of lichenoid dermatosis, being characterized by the presence of a dense dermal cell infiltrate. Although most cases of LP are idiopathic, infectious and drug-related factors must also be considered in the aetiology. In this context, the occurrence of LP and lichenoid drug eruptions following different types of vaccination is a possible event. Therefore, the aim of our review is to provide a broad perspective to clinicians by analysing the current literature of cases of LP and lichenoid eruptions following COVID-19 vaccination, and also investigating the possible pathogenetic mechanisms underlying this phenomenon. In total, 61 cases of LP and lichenoid eruption following COVID-19 vaccination have been collected. However, the number of cases of LP and lichenoid drug eruption is extremely low compared with the number of vaccines administered overall, suggesting that the risk of LP and lichenoid eruption following COVID-19 vaccination is extremely low. Certainly, further studies are desirable to identify the population most at risk and the possibility of taking preventive measures.
Transportable, portable, wearable and (partially) implantable haemodialysis systems: comparison of technologies and readiness levels
Authors: Wieringa Fokko P , Bolhuis Dian , Søndergaard Henning , Ash Stephen R , Cummins Cian , Gerritsen Karin G F , Vollenbroek Jeroen , Irmak Tugrul 
Published: August 2024

ABSTRACT

Background
Dialysis modalities and their various treatment schedules result from complex compromises (‘trade-offs’) between medical, financial, technological, ergonomic, and ecological factors. This study targets summarizing the mutual influence of these trade-offs on (trans)portable, wearable, or even (partially) implantable haemodialysis (HD) systems, identify what systems are in development, and how they might improve quality of life (QoL) for patients with kidney failure.

Methods
HD as defined by international standard IEC 60601–2-16 was applied on a PUBMED database query regarding (trans)portable, wearable, and (partly) implantable HD systems. Out of 159 search results, 24 were included and scanned for specific HD devices and/or HD systems in development. Additional information about weight, size, and development status was collected by the internet and/or contacting manufacturers. International airplane hand baggage criteria formed the boundary between transportable and portable. Technology readiness levels (TRLs) were assigned by combining TRL scales from the European Union and NATO medical staff.

Results
The query revealed 13 devices/projects: seven transportable (six TRL9, one TRL5); two portable (one TRL6–7, one TRL4); two wearable (one TRL6, one frozen); and two partly implantable (one TRL4–5, one TRL2–3).

Discussion
Three main categories of technical approaches were distinguished: single-pass, dialysate regenerating, and implantable HD filter with extracorporeal dialysate regeneration (in climbing order of mobility).

Conclusions
Kidneys facilitate mobility by excreting strongly concentrated waste solutes with minimal water loss. Mimicking this kidney function can increase HD system mobility. Dialysate-regenerating HD systems are enablers for portability/wearability and, combined with durable implantable HD filters (once available), they may enable HD without needles or intravascular catheters. However, lack of funding severely hampers progress.
Burden of risk factors in women and men with unrecognized myocardial infarction: a systematic review and meta-analysis
Authors: van Oortmerssen Julie A E , Ntlapo Noluthando , Tilly Martijn J , Bramer Wichor M , den Ruijter Hester M , Boersma Eric , Kavousi Maryam , Roeters van Lennep Jeanine E 
Published: August 2024

Abstract
Unrecognized myocardial infarction (MI) is an MI that remains undetected in the acute phase and is associated with an unfavourable prognosis. With this systematic review and meta-analysis, we evaluated the burden of cardiovascular risk factors in individuals with unrecognized MI. We searched general population-based cohort studies diagnosing unrecognized MI by electrocardiogram or myocardial imaging up to 24 November 2023. Pooled mean differences (MDs) or risk ratios (RRs) with 95% confidence intervals (CIs) were determined, and random-effects meta-analyses were performed. Fourteen cohort studies were included involving 200 450 individuals (mean age 62.8 ± 9.9 years, 56.0% women), among which 4322 (2.2%) experienced unrecognized MI (mean age 66.3 ± 8.2 years, 47.8% women) and 4653 (2.1%) recognized MI (mean age 68.5 ± 7.3 years, 33.8% women). Compared to individuals without MI, those with unrecognized MI had higher body mass index (MD 0.27, 95% CI 0.16–0.39) and systolic blood pressure (MD 4.48, 95% CI 2.81–6.15) levels, and higher prevalence of hypertension (RR 1.27, 95% CI 1.06–1.51) and diabetes mellitus (RR 1.67, 95% CI 1.36–2.06). Furthermore, individuals with unrecognized MI had lower prevalence of hypertension (RR 0.92, 95% CI 0.88–0.97) and diabetes mellitus (RR 0.80, 95% CI 0.70–0.92). Individuals with unrecognized MI are characterized by a substantial burden of metabolic risk factors. Our findings suggest insufficient recognition and management of cardiovascular risk factors among individuals with unrecognized MI.
Oligonucleotide-based CRISPR-Cas9 toolbox for efficient engineering of Komagataella phaffii
Authors: Strucko Tomas , Gadar-Lopez Adrian-E , Frøhling Frederik B , Frost Emma T , Iversen Esther F , Olsson Helen , Jarczynska Zofia D , Mortensen Uffe H 
Published: August 2024

Abstract
Komagataella phaffii (Pichia pastoris) is a methylotrophic yeast that is favored by industry and academia mainly for expression of heterologous proteins. However, its full potential as a host for bioproduction of valuable compounds cannot be fully exploited as genetic tools are lagging behind those that are available for baker’s yeast. The emergence of CRISPR-Cas9 technology has significantly improved the efficiency of gene manipulations of K. phaffii, but improvements in gene-editing methods are desirable to further accelerate engineering of this yeast. In this study, we have developed a versatile vector-based CRISPR-Cas9 method and showed that it works efficiently at different genetic loci using linear DNA fragments with very short targeting sequences including single-stranded oligonucleotides. Notably, we performed site-specific point mutations and full gene deletions using short (90 nt) single-stranded oligonucleotides at very high efficiencies. Lastly, we present a strategy for transient inactivation of nonhomologous end-joining (NHEJ) pathway, where KU70 gene is disrupted by a visual marker (uidA gene). This system enables precise CRISPR-Cas9-based editing (including multiplexing) and facilitates simple reversion to NHEJ-proficient genotype. In conclusion, the tools presented in this study can be applied for easy and efficient engineering of K. phaffii strains and are compatible with high-throughput automated workflows.
EARA2024: a new radially anisotropic seismic velocity model for the crust and upper mantle beneath East Asia and Northwestern pacific subduction zones
Authors: Xi Ziyi , Chen Min , Wei Songqiao Shawn , Li Jiaqi , Zhou Tong , Wang Baoshan , Kim YoungHee 
Published: August 2024

SUMMARY
We present a new 3-D radially anisotropic seismic velocity model EARA2024 of the crust and mantle beneath East Asia and the northwestern Pacific using adjoint full-waveform inversion tomography. We construct the EARA2024 model by iteratively minimizing the waveform similarity misfit between the synthetic and observed waveforms from 142 earthquakes recorded by about 2000 broad-band stations in East Asia. Compared to previous studies, this new model renders significantly improved images of the subducted oceanic plate in the upper mantle, mantle transition zone, and uppermost lower mantle along the Kuril, Japan, Izu-Bonin and Ryukyu Trenches. Complex slab deformation and break-offs are observed at different depths. Moreover, our model provides new insights into the origins of intraplate volcanoes in East Asia, including the Changbaishan, Datong-Fengzhen, Tengchong and Hainan volcanic fields.
High-precision vertical deformation of the Chinese mainland constrained by levelling and GNSS data
Authors: Wu Yanqiang , Su Guangli , Nie Jianliang , Chen Changyun , Chen Zhaohui , Yu Huazhi , Yin Haiquan , Chang Liu , Tang Zheng , Pang Yajin , Liang Hongbao , Bo Wanju 
Published: August 2024

SUMMARY
A high-precision and high-resolution vertical velocity for the Chinese mainland is obtained by integrating precise levelling and Global Navigation Satellite System data, using a Helmert joint adjustment method. The results show that the surface vertical rates range between −3.0 and 3.9 mm yr−1 with continuous deformation in most areas, except the obvious subsidence at the rates of −15.0 to −94.2 mm yr−1 induced by groundwater exploitation in the North China Plain. Particularly, the central and southern Tibet, Tien Shan, Alashan, Ordos, eastern Cathaysia and Northeast China uplift at the rates of 0.5–3.9 mm yr−1; the southeastern Tibetan Plateau, Sichuan basin and Yangtze block are dominated by surface subsidence at the rates of −3.3 to −0.5 mm yr−1. Furthermore, the vertical rates vary little between the eastern and western regions of the Chinese mainland despite their pronounced differences in horizontal deformations. The effects of gravity isostasy and non-tectonic factors, including the environmental mass loads, Glacier Isostatic Adjustment (GIA), poroelastic expansion/compression, and mining operations have partially contributed to the vertical deformation of the Chinese mainland. Overall, this velocity reflects the complicated deformation features induced by the multiple geodynamic processes of the Chinese mainland. These geodynamic processes include isostasy, orogenic processes and geothermal anomalies associated with slab subduction/plate collision.
Potential therapeutic use of dermaseptin S4 from the frog Phyllomedusa sauvagii and its derivatives against bacterial pathogens in fish
Authors: Braik Afef , Serna-Duque John Alberto , Nefzi Adel , Aroui Sonia , Esteban María Ángeles 
Published: August 2024

Abstract

Aim
Dermaseptins are one of the main families of antimicrobial peptides (AMPs) derived from the skin secretions of Hylidae frogs. Among them, dermaseptin S4 (DS4) is characterized by its broad-spectrum of activity against bacteria, protozoa, and fungi. In this study, the physicochemical properties of the native peptide DS4 (1–28) and two derivatives [DS4 (1–28)a and DS4 (1–26)a] isolated from the skin of the frog Phyllomedusa sauvagii were investigated and their antimicrobial properties against two marine pathogenic bacteria (Vibrio harveyi and Vibrio anguillarum) were examined.

Methods and results
The results indicate that the peptide DS4 (1–26)a has high-antibacterial activity against the tested strains and low-hemolytic activity (&lt;30% lysis at the highest tested concentration of 100 µg/mL) compared to the other two peptides tested. In addition, all three peptides affect the membrane and cell wall integrity of both pathogenic bacteria, causing leakage of cell contents, with DS4 (1–26)a having the most severe impact. These skills were corroborated by transmission electron microscopy and by the variation of cations in their binding sites due to the effects caused by the AMPs.

Conclusions
These results suggest that DS4 and its derivatives, in particular the truncated and amidated peptide DS4 (1–26)a could be effective in the treatment of infections caused by these marine pathogenic bacteria. Future studies are required to validate the use of DS4 in vivo for the prevention of bacterial diseases in fish.
Brighteness-dependent visual attractiveness of the human body for horse flies (Diptera: Tabanidae): a field experiment
Authors: Balogh Attila , Kúdela Matúš 
Published: August 2024

Abstract
The landing patterns of blood-sucking females (Diptera: Tabanidae) are largely influenced by their visual perceptions. When attacking humans, the shape of different body parts and overall brightness of the body could be the factors determining the place of blood-sucking. The visual attractiveness of the human body for tabanids was investigated through a black and a white mannequin in the Danube floodplain, Slovakia. The mannequins were covered by glue once a week. On both of the mannequins, 332 horse flies were stuck. The trapped horse flies on the mannequins belong to the genera Tabanus Linnaeus, 1758, Hybomitra Enderlein, 1922, Chrysops Meigen, 1803, Haematopota Linnaeus, 1758 and Atylotus (Linnaeus, 1767). Based on the trapped tabanids, the black mannequin is 6.06 times more attractive than the white one. The most tabanid carcasses were found on the lower limbs (56.32%) and the least occurred on the head (2.1%), the difference in their occurrence between the lower limbs and head of both mannequins was significant (P &lt; 0.001). A similar significant difference was observed on certain parts of both mannequins on the taxonomical level of the genera Tabanus, Hybomitra, and Atylotus, the carcasses of which aggregated mostly on the lower limbs, rather than on the upper limbs and head.
Molecular and serological detection of Leishmania infantum (Trypanosomatida: Trypanosomatidae) in domestic dogs in Manaus city, Amazonas, Brazil
Authors: Nascimento de Campos Hevila Gabrieli , Gennari Solange Maria , da Silva Ryan Emiliano , Soares Herbert Sousa , Costa Jaciara de Oliveira Jorge , de Azevedo Sergio Santos , Marcili Arlei 
Published: August 2024

Abstract
Leishmaniasis are zoonosis widely spread in Brazil, caused by the protozoan of the genus Leishmania, which includes several species. The disease manifests itself in the visceral or tegumentary form, and the main reservoir is the dogs. Manaus is the largest city in the Brazilian Amazon region, and despite the importance of the municipality, practically nothing is known about leishmaniosis in humans and animals. The objective of this study was to evaluate the occurrence and risk factors associated with the presence of Leishmania infantum in domiciliated dogs from Manaus. Molecular (polymerase chain reaction) and serological (immunofluorescent antibody test) methods were used as an indication of the circulation of the parasite. Blood samples for 154 domiciled dogs were obtained, and prevalence ratio and analysis of the variables were performed. Serum antibodies anti-Leishmania spp. were detected in 20.8% (95% CI: 14.4%–27.2%). Access to the street and zone of residence (P &lt; 0.01) were associated with higher seropositivity. Molecular diagnosis for L. infantum detected positivity in 60 (39%) of the 154 (95% CI: 31.3%–46.7%) animals, and the variables street access, contact with dogs, and zone of residence were associated with higher frequencies of positivity (P &lt; 0.05). Both serology and molecular diagnosis detected positive dogs in the municipality. This is the first description of the circulation of L. infantum infecting dogs in Manaus. As the municipality is classified as nonendemic, studies of isolation and characterization of the isolate must be done urgently.
Narrating the Client: How stories of parental influence impact teacher professionalism
Authors: Eklund Sanna 
Published: August 2024

Abstract
This article examines how teachers engage in symbolic institutional work to address client influence, and how this impacts teacher professionalism. The study delves into an intriguing empirical field, using the Swedish school system as an illustrative case for studying the development of professionalism within a highly marketized context. The research employed interviews, observations, and shadowing, enabling a deeper understanding of the symbolic institutional work in a complex institutional environment where market and professional logic collide. The findings demonstrate how teachers utilize a narrative of a threatening and demanding client, which helps them distance themselves from market logic and resist adapting to it in their professionalism. However, there are also indications of a different narrative, where some teachers embrace and integrate client influence as a natural part of their professionalism. Additionally, there is also a form of ambivalence, where teachers are moving between different narratives. By investigating how professionals engage in these narratives, the article provides insights into understudied dimensions within the concept of professionalism. While the existence of different narratives highlights the complexity and fragility of institutional work, the inclination towards distancing from clients illustrates a preservation of traditional professionalism rather than a shift towards the ‘new professionalism’ described in previous literature.
Achieving a cure for anastomotic leakage following laparoscopic low anterior resection for rectal cancer using an endoscopic closure device, a MANTIS clip
Authors: Horikawa Daisuke , Takahata Hiroki , Fujiwara Yasuhiro 
Published: August 2024

Abstract
Anastomotic leakage (AL) following low anterior resection (LAR) for rectal cancer is a major complication. While most reports focus on the closure of AL using over-the-scope clip (OTSC), few reports are available on the use of through-the-scope clip (TTSC). This is because TTSC is not typically designed for full-thickness closure, unlike OTSC. However, a MANTIS clip, categorized as TTSC, is indicated for full-thickness closure. A 73-year-old man diagnosed with AL 7 days postoperatively following laparoscopic LAR underwent laparoscopic drainage and ileostomy the next day. Although the drainage led to the shrinkage of the fistula, it persisted even after 2 months. Consequently, the fistula orifice was closed using a MANTIS clip under colonoscopy and radiography. Two days later, the patient was discharged. The drain was withdrawn cautiously to prevent residual fistula and removed completely on day 29. This report highlights our experience in using a MANTIS clip for AL following LAR.
Prospects for neutron star parameter estimation using gravitational waves from f modes associated with magnetar flares
Authors: Ball Matthew , Frey Raymond , Merfeld Kara 
Published: August 2024

ABSTRACT
Magnetar vibrational modes are theorized to be associated with energetic X-ray flares. Regular searches for gravitational waves from these modes have been performed by Advanced LIGO (Laser Interferometer Gravitational-wave Observatory) and Advanced Virgo, with no detections so far. Presently, search results are given in upper limits on the root sum square of the integrated gravitational-wave strain. However, the increased sensitivity of current detectors and the promise of future detectors invite the consideration of more astrophysically motivated methods. We present a framework for augmenting gravitational-wave searches to measure or place direct limits on magnetar astrophysical properties in various search scenarios using a set of phenomenological and analytical models.
Probing the spatial and velocity anisotropies in stellar haloes from the Aquarius simulations
Authors: Mondal Amit , Pandey Biswajit 
Published: August 2024

ABSTRACT
We analyse the spatial anisotropy and the velocity anisotropy in a set of mock stellar haloes from the Aquarius simulations. The spatial anisotropy in each mock stellar halo rises progressively with the increasing distance from the halo centre, eventually reaching a maximum near the periphery. Excluding the bound satellites leads to a significant reduction of the spatial anisotropy in each halo. We compare the measured anisotropy in the mock stellar haloes with that from their sphericalized versions where all the shape- and substructure-induced anisotropies are erased. The growth of spatial anisotropy persists throughout the entire halo when the bound satellites are present but remains limited within the inner halo (${\lt} 60 \, {h^{-1}\, {\rm kpc}}$) after their exclusion. This indicates that the spatial anisotropy in the inner halo is induced by the diffuse substructures and the halo shape, whereas the outer halo anisotropy is dominated by the bound satellites. We find that the outer parts of the stellar halo are kinematically colder than the inner regions. The stellar orbits are predominantly radial, but they become rotationally dominated at certain radii that are marked by the prominent dips in the velocity anisotropy. Most of these dips disappear after the removal of the satellites. A few shallow dips arise occasionally due to the presence of diffuse streams and clouds. Our analysis suggests that a combined study of the spatial and velocity anisotropies can reveal the structure and the assembly history of the stellar haloes.
BASILISK II. Improved constraints on the galaxy–halo connection from satellite kinematics in SDSS
Authors: Mitra Kaustav , van den Bosch Frank C , Lange Johannes U 
Published: August 2024

ABSTRACT
Basilisk is a novel Bayesian hierarchical method for inferring the galaxy–halo connection, including its scatter, using the kinematics of satellite galaxies extracted from a redshift survey. In this paper, we introduce crucial improvements, such as updated central and satellite selection, advanced modelling of impurities and interlopers, extending the kinematic modelling to fourth order by including the kurtosis of the line-of-sight velocity distribution, and utilizing satellite abundance as additional constraint. This drastically enhances Basilisk’s performance, resulting in an unbiased recovery of the full conditional luminosity function (central and satellite) and with unprecedented precision. After validating Basilisk’s performance using realistic mock data, we apply it to the SDSS-DR7 data. The resulting inferences on the galaxy–halo connection are consistent with, but significantly tighter than, previous constraints from galaxy group catalogues, galaxy clustering, and galaxy–galaxy lensing. Using full projected phase-space information, Basilisk breaks the mass-anisotropy degeneracy, thus providing precise global constraint on the average orbital velocity anisotropy of satellite galaxies across a wide range of halo masses. Satellite orbits are found to be mildly radially anisotropic, in good agreement with the mean anisotropy for subhaloes in dark matter-only simulations. Thus, we establish Basilisk as a powerful tool that is not only more constraining than other methods on similar volumes of data, but crucially, is also insensitive to halo assembly bias which plagues the commonly used techniques like galaxy clustering and galaxy–galaxy lensing.