bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of host ecology and phylogeny on gut microbiota (non)parallelism across birds and mammals
Authors: Härer Andreas , Rennison Diana J. 
Published: December 2023

ABSTRACT
The gut microbiota plays a crucial role in the biological function of their hosts since bacteria provide nutrient processing, protection against pathogens, and modulation of the immune system. Thus, as organisms adapt to different ecological niches, their gut microbial communities are thought to change in response to novel environmental conditions. Quantifying the direction and magnitude of gut microbiota changes associated with ecological niche offers valuable insights into the predictability of gut microbial community change accompanying shifts in host ecology. We used multivariate vector analysis to assess the (non)parallelism of gut microbiota community composition associated with host occupancy of a similar niche. We studied gut microbiota (non)parallelism across an extensive data set of 53 mammalian and 50 avian host species. Our results suggest that parallel shifts in host trophic ecology are associated with greater gut microbiota parallelism, whereas we could not find evidence for a clear effect of host phylogeny. Furthermore, parallelism was generally stronger when estimated from inferred metagenome function compared with gut microbiota taxonomic composition, suggesting that functional redundancy among bacterial lineages might obscure the signature of adaptive gut microbiota changes. Notably, a substantial proportion of the variation in gut microbiota (non)parallelism was not explained by host trophic ecology or phylogeny. Thus, we encourage future microbiota studies to use quantitative analyses along with additional ecological and host-associated data to obtain a comprehensive understanding of the factors shaping the direction and magnitude of gut microbiota changes associated with ecological divergence.

IMPORTANCE
What are the roles of determinism and contingency in evolution? The paleontologist and evolutionary biologist Stephen J. Gould raised this question in his famous thought experiment of “replaying life’s tape.” Settings where independent lineages have repeatedly adapted to similar ecological niches (i.e., parallel evolution) are well suited to address this question. Here, we quantified whether repeated ecological shifts across 53 mammalian and 50 avian host species are associated with parallel gut microbiota changes. Our results indicate that parallel shifts in host diet are associated with greater gut microbiota parallelism (i.e., more deterministic). While further research will be necessary to obtain a comprehensive picture of the circumstances under which deterministic gut microbiota changes might be expected, our study can be instrumental in motivating the use of more quantitative methods in microbiota research. This, in turn, can help us better understand microbiota dynamics during adaptive evolution of their hosts.
The ER-Golgi transport of influenza virus through NS1-Sec13 association during virus replication
Authors: Chua Sonja C. J. H. , Cui Jianzhou , Sachaphibulkij Karishma , Tan Isabelle Siang Ling , Tan Hui Qing , Lim Hong Meng , Engelberg David , Lim Lina H. K. 
Published: December 2023

ABSTRACT
Influenza A virus is a respiratory virus that can cause complications such as acute bronchitis and secondary bacterial pneumonia. Drug therapies and vaccines are available against influenza, albeit limited by drug resistance and the non-universal vaccine administration. Hence there is a need for host-targeted therapies against influenza to provide an effective alternative therapeutic target. Sec13 was identified as a novel host interactor of influenza. As Sec13 is a member of the nuclear pore complex and coat protein complex II (COPII) vesicles, localization of both Sec13 and non-structural protein 1 (NS1) in the nucleus, endoplasmic reticulum (ER), COPII vesicles (ER-to-Golgi transport), and Golgi was studied during infection. Sec13 is associated with ER, COPII, and Golgi in infected lung epithelial cells and not the nucleus during PR8 infection. This observation would imply the functional role of Sec13 in the COPII vesicles (ER-to-Golgi transport). Moreover, the colocalization of NS1 and Sec13 were correlated at several time points of infection, indicating the function of Sec13 during influenza infection. Inhibiting the ER-to-Golgi transport and silencing Sec13 decreased viral titers, whereas overexpressing Sec13 increased viral titers. Hence, we propose that the ER-to-Golgi transport is an important pathway of viral replication and viral export, and specifically, Sec13 has a functional role in influenza replication and virulence.

IMPORTANCE
Influenza A virus is a respiratory virus that can cause complications such as acute bronchitis and secondary bacterial pneumonia. Drug therapies and vaccines are available against influenza, albeit limited by drug resistance and the non-universal vaccine administration. Hence there is a need for host-targeted therapies against influenza to provide an effective alternative therapeutic target. Sec13 was identified as a novel host interactor of influenza. Endoplasmic reticulum-to-Golgi transport is an important pathway of influenza virus replication and viral export. Specifically, Sec13 has a functional role in influenza replication and virulence.
Cenozoic dextral transpressional tectonics in the northwestern Qaidam Basin, northern Tibet: Evidence from paleomagnetic and kinematic analysis of the arcuate belts
Authors: Peng Luying , Yu Xiangjiang , Huang Baochun , Cheng Feng , Yang Yizhou , Wu Jiawei , Yi Kexin , Guo Zhaojie 
Published: November 2023

Abstract
The mechanisms by which complex intracontinental deformation in the northern Tibetan Plateau was accommodated since the India-Asia collision remain debated. Characterization of the formation of arcuate structures in northern Tibet provides important constraints on this debate. We conducted a new paleomagnetic study on the mid- to late Miocene strata along the curved Lenghu-Nanbaxian and Eboliang-Hulushan belts of the Qaidam Basin, northern Tibet. Our results revealed that there is nonsignificant relative rotation within localities along these arcuate belts, which yielded a common mean direction of declination (D) = 3.6°, inclination (I) = 35.7° (α95 = 2.4°) after tilt correction, suggesting negligible Neogene vertical-axis rotation along the arcuate belts in the Qaidam Basin. Outcropped fault striations and the positive flower structures indicate dextral strike-slip–dominated motion along the faults since the mid- to late Miocene. By integrating the paleomagnetic results with the kinematics of these associated faults, we ruled out the possibility that these curved belts formed due to the frictional drag of the Altyn Tagh fault or due to differential shortening across the Qaidam Basin. Instead, we attribute the formation of these nonrotational arcuate belts to dextral transpressional deformation occurring within the basin since the mid- to late Miocene. Different from the orogenic belts in the northern Tibetan Plateau that absorbed postcollisional convergence through block rotation, crustal shortening, and lateral extrusion, the Qaidam Basin has also accommodated significant intracontinental deformation in the northern Tibetan Plateau through transpressional deformation within the basin. This inference underscores the importance of recognizing crustal extrusion within rigid blocks as a record of intracontinental deformation in the northern Tibetan Plateau.
Transgender identity in young people and adults recorded in UK primary care electronic patient records: retrospective, dynamic, cohort study
Authors: McKechnie Douglas Gordon John , O'Nions Elizabeth , Bailey Julia , Hobbs Lorna , Gillespie Frank , Petersen Irene 
Published: November 2023

ObjectivesTo quantify the change in proportion of young people and adults identified as transgender in UK primary care records and to explore whether rates differ by age and socioeconomic deprivation.DesignRetrospective, dynamic, cohort study.SettingIQVIA Medical Research Data, a database of electronic primary care records capturing data from 649 primary care practices in the UK between 1 January 2000 and 31 December 2018.Participants7 064 829 individuals aged 10-99 years, in all four UK countries.Main outcome measuresDiagnostic codes indicative of transgender identity were used. Sex assigned at birth was estimated by use of masculinising or feminising medication and procedural/diagnostic codes.Results2462 (0.03%) individuals had a record code indicating a transgender identity. Direction of transition could be estimated for 1340 (54%) people, of which 923 were assigned male at birth, and 417 were assigned female at birth. Rates of recording in age groups diverged substantially after 2010. Rates of the first recording of codes were highest in ages 16-17 years (between 2010 and 2018: 24.51/100 000 person years (95% confidence interval 20.95 to 28.50)). Transgender codes were associated with deprivation: the rate of the first recording was 1.59 (95% confidence interval 1.31 to 1.92) in the most deprived group in comparison with the least deprived group. Additionally, the rate ratio of the proportion of people who identified as transgender was 2.45 (95% confidence interval 2.28 to 2.65) in the most deprived group compared with the least deprived group. Substantial increases were noted in newly recorded transgender codes over time in all age groups (1.45/100 000 person years in 2000 (95% confidence interval 0.96 to 2.10) to 7.81/100 000 person years in 2018 (6.57 to 9.22)). In 2018, the proportion of people with transgender identity codes was highest in the age groups 16-17 years (16.23 per 10 000 (95% confidence interval 12.60 to 20.57)) and 18-29 years (12.42 per 10 000 (11.06 to 13.90)).ConclusionThe rate of transgender identity recorded in primary care records has increased fivefold from 2000 to 2018 and is highest in the 16-17 and 18-29 age groups. Transgender diagnostic coding is associated with socioeconomic deprivation and further work should investigate this association. Primary and specialist care should be commissioned accordingly to provide for the gender specific and general health needs of transgender people.
Symptoms and signs in patients with heart failure: association with 3-month hospitalisation and mortality
Authors: Ali Mohammad Rizwan , Lam Carolyn S P , Strömberg Anna , Hand Simon P P , Booth Sarah , Zaccardi Francesco , Squire Iain , McCann Gerry P , Khunti Kamlesh , Lawson Claire Alexandra 
Published: December 2023

ObjectivesTo determine the association between symptoms and signs reported in primary care consultations following a new diagnosis of heart failure (HF), and 3-month hospitalisation and mortality.DesignNested case–control study with density-based sampling.SettingClinical Practice Research Datalink, linked to hospitalisation and mortality (1998–2020).ParticipantsDatabase cohort of 86 882 patients with a new HF diagnosis. In two separate analyses for (1) first hospitalisation and (2) death, we compared the 3-month history of symptoms and signs in cases (patients with HF with the event), with their respective controls (patients with HF without the respective event, matched on diagnosis date (±1 month) and follow-up time). Controls could be included more than once and later become a case.Main outcome measuresAll-cause, HF and non-cardiovascular disease (non-CVD) hospitalisation and mortality.ResultsDuring a median follow-up of 3.22 years (IQR: 0.59–8.18), 56 677 (65%) experienced first hospitalisation and 48 146 (55%) died. These cases were matched to 356 714 and 316 810 HF controls, respectively. For HF hospitalisation, the strongest adjusted associations were for symptoms and signs of fluid overload: pulmonary oedema (adjusted OR 3.08; 95% CI 2.52, 3.64), shortness of breath (2.94; 2.77, 3.11) and peripheral oedema (2.16; 2.00, 2.32). Generic symptoms also showed significant associations: depression (1.50; 1.18, 1.82), anxiety (1.35; 1.06, 1.64) and pain (1.19; 1.10, 1.28). Non-CVD hospitalisation had the strongest associations with chest pain (2.93; 2.77, 3.09), fatigue (1.87; 1.73, 2.01), general pain (1.87; 1.81, 1.93) and depression (1.59; 1.44, 1.74).ConclusionsIn the primary care HF population, routinely recorded cardiac and non-specific symptoms showed differential risk associations with hospitalisation and mortality.
Targeting integrin α5 in fibroblasts potentiates colorectal cancer response to PD-L1 blockade by affecting extracellular-matrix deposition
Authors: Lu Ling , Gao Yaohui , Huang Dengfeng , Liu Hu , Yin Dingzi , Li Man , Zheng Jiayi , Wang Shufei , Wu Weijun , Zhao Li , Bi Dexi , Zhang Youhua , Song Feifei , Xie Ruting , Wang Jifeng , Qin Huanlong , Wei Qing 
Published: December 2023

BackgroundOne reason patients with cancer cannot benefit from immunotherapy is the lack of immune cell infiltration in tumor tissues. Cancer-associated fibroblasts (CAFs) are emerging as central players in immune regulation that shapes tumor microenvironment (TME). Earlier we reported that integrin α5 was enriched in CAFs in colorectal cancer (CRC), however, its role in TME and cancer immunotherapy remains unclear. Here, we aimed to investigate the role for integrin α5 in fibroblasts in modulating antitumor immunity and therapeutic efficacy combined with checkpoint blockade in CRC.MethodsWe analyzed the CRC single-cell RNA sequencing (scRNA-seq) database to define the expression ofITGA5in CRC tumor stroma. Experimentally, we carried out in vivo mouse tumor xenograft models to confirm the targeting efficacy of combined α5β1 inhibition and anti-Programmed death ligand 1 (PD-L1) blockade and in vitro cell-co-culture assay to investigate the role of α5 in fibroblasts in affecting T-cell activity. Clinically, we analyzed the association between α5 expression and infiltrating T cells and evaluated their correlation with patient survival and immunotherapy prognosis in CRC.ResultsWe revealed thatITGA5was enriched inFAP-CAFs. BothITGA5knockout fibroblasts and therapeutic targeting of α5 improved response to anti-PD-L1 treatment in mouse subcutaneous tumor models. Mechanistically, these treatments led to increased tumor-infiltrating CD8+T cells. Furthermore, we found that α5 in fibroblasts correlated with extracellular matrix (ECM)-related genes and affected ECM deposition in CRC tumor stroma. Both in vivo analysis and in vitro culture and cell killing experiment showed that ECM proteins and α5 expression in fibroblasts influence T-cell infiltration and activity. Clinically, we confirmed that high α5 expression was associated with fewer CD3+T and CD8+T cells, and tissues with low α5 and high CD3+T levels correlated with better patient survival and immunotherapy response in a CRC cohort with 29 patients.ConclusionsOur study identified a role for integrin α5 in fibroblasts in modulating antitumor immunity by affecting ECM deposition and showed therapeutic efficacy for combined α5β1 inhibition and PD-L1 blockade in CRC.
Tolerability of low to moderate biomechanical stress during leisure sport activity in patients with psoriasis and psoriatic arthritis
Authors: Fagni Filippo , Mutlu Melek Yalcin , Temiz Selahattin Alp , Minopoulou Ioanna , Krieter Manuel , Schett Georg , Kleyer Arnd , Simon David , Hueber Axel J 
Published: December 2023

ObjectivesTo assess the impact of low to moderate biomechanical stress on entheses in patients with psoriasis and psoriatic arthritis (PsA).MethodsWe conducted a prospective interventional study on a cohort of psoriasis and PsA patients who underwent a 60 min badminton training session. Pain assessment by Visual Analogue Scale (VAS), physical examination of 29 entheses (SPARCC, LEI, MASES) and bilateral ultrasound at the lateral humeral epicondyle, inferior patellar pole and Achilles tendon were performed before and after training. Ultrasound changes were assessed using the OMERACT scoring system. A follow-up assessment of pain and adverse events was performed at 1 week.ResultsSixteen patients were included (n=7 PsA; n=9 psoriasis) and 196 entheseal ultrasound scans were acquired. At baseline, median VAS pain (IQR) was 0.5 cm (0–2.3) and the total number of tender entheses was 12/464. Mean (min; max) Disease Activity Index for Psoriatic Arthritis was 6.1 (0.8; 19) and 5/7 PsA patients had an Minimal Disease Activity status. After training, no significant change in VAS pain (0.0 cm (0.0–2.0)) nor in tender entheses (13/464) emerged. Four patients (n=2 PsA, n=2 psoriasis) developed a grade-1 power Doppler-signal at six entheses, which, however, remained non-tender. At 1 week, median VAS pain remained stable (0.0 cm (0.0–3.0); p>0.05) and only one participant with active PsA at baseline reported increased arthralgias in three joints.ConclusionsLow to moderate physical strain, as in the context of leisure sport activity, seems well tolerated in psoriatic patients without increases in tenderness, pain and ultrasound-proven inflammation. Evidence-based recommendations for physical activity in PsA are direly needed and larger controlled studies should be conducted to define safe exercise thresholds.
Emergency Aesthetics: The Case of the Four Faces of Omarska
Authors: Glisic Iva , Puric Biljana 
Published: November 2023

Abstract
This article examines how contemporary artists from the Western Balkans have sought to engage with the legacy of ethnonationalist violence. While attempts to examine and openly discuss war crimes that occurred in this region during the 1990s have largely been undermined by populist politics in successor states, the domain of art has provided a critical platform for disrupting the official erasure of these atrocities. This investigation focuses on the Four Faces of Omarska art collective, whose members examine the war crimes that occurred following the break-up of socialist Yugoslavia by studying the transformation of the Omarska site in north-western Bosnia – a location that has variously served as a mining complex, a death camp, and a set for the filming of an ‘ethno-blockbuster.’ In providing a comprehensive (art) historical analysis of their practice, the article considers the collective's public engagement strategies by invoking Santiago Zabala's concept of ‘emergency aesthetics’ as a method for countering the political erasure of urgent issues. This analysis reveals that the significance of the Four Faces of Omarska project extends beyond its immediate post-socialist context, and indeed provides a model of creative practice fit for our era of planetary crisis.
Bags of Stories: Thinking with Household Casebearers in the Anthropocene
Authors: Hao Tan Zi 
Published: November 2023

Abstract
Household casebearers are a genus of moths primarily distinguished by the spindle-shaped cases they carry and live in throughout their larval life. The cases, woven from household dust, typically comprise an array of materials from textile fibers to dead insect parts. As they thrive in domestic spaces in tropical climates, they are commonly viewed as a domestic pest. Anthropocentrism as such has led to a fundamental imbalance of knowledge concerning these creatures: we are more knowledgeable in their capacity for damage than we are in understanding how they live, even as we cohabit with them very closely, at home. In presenting a series of macro photography of their larval cases, this project invites readers to be attentive to the material and ecological entanglements on display on their intricate creations. The home is already a wilderness as household casebearers rebuild their houses from the dusty ruins of ours.
Deadly nuts – detection of 3-nitropropionic acid in coconuts
Authors: Ringsborg Westphal K. , Vittrup Andersen N. , Uttrup Dideriksen B. , Filtenborg Gunggaard A. , Duus M.A. , Sondergaard T.E. 
Published: December 2023

Abstract
The secondary metabolite 3-nitropropionic acid (3-NPA) is produced by certain fungi. The metabolite is a potent toxin which inhibits the citric acid cycle. A medical case from 2021 described a 69-year-old Danish man who ingested 3-nitropropionic acid contaminated coconut water. The man died 26 hours after ingestion. Subsequent analysis identified Apiospora saccharicola as the fungi responsible for synthesising 3-NPA in the coconut. The metabolic pathway for 3-NPA is unknown but is thought to be activated by adverse growth conditions. This study aimed to confirm that Apiospora can produce 3-NPA within coconuts and develop a quick and easy method for detection of 3-NPA in coconut water using 1H NMR. This method can possibly aid in detection of 3-NPA in contaminated groceries, such as coconut water.
The Infinite Task of Genealogy
Authors: Reichmuth Stefan 
Published: December 2023

Abstract
The Indian polymath Muḥammad Murtaḍà al-Zabīdī (1145/1732-1205/1791) studied in Zabīd in the Yemen and then in the Hijaz before he chose to move to Egypt, where he embarked upon a unique career as a leading ḥadīṯ scholar, lexicographer, genealogist and Sufi traditionist of his time. By his philological-cum-ḥadīṯ-oriented activities which were combined with his comprehensive interest in a genealogy of Muslim culture, he greatly fascinated his contemporaries.
Genealogical research, recording and writing were a central part of al-Zabīdī’s scholarly interest, and he became a widely respected authority in this field. He was contacted and consulted by scholars and visitors from very distant regions, collecting genealogical information from them and, at the same, responding to their queries about the past of their families and ethnic groups.
In the following the central project of al-Zabīdī’s own genealogical research and writing, a commentary and extension of an important older genealogical book (al-Naǧafī’s al-Mušaǧǧar al-kaššāf) will be described and scrutinized. Like other works of al-Zabīdī, this commentary has remained unfinished, and even the manuscript situation of al-Naǧafī’s text itself remains highly complex. It is hoped to bring out the specific character of al-Zabīdī’s own genealogical approach, which aimed at a universal and, at the same time, updated genealogical framework for the Muslim world, and which perhaps fell victim of the boundless field into which he had plunged.
Animal welfare science: an integral piece of sustainable insect agriculture
Authors: Barrett M. , Adcock S.J.J. 
Published: November 2023

Abstract
The insects as food and feed (IAFF) industry represents one of the largest undertakings of industrial livestock rearing in human history, with at least a trillion animals reared each year and massive growth potential. As other livestock industries have grown, animal welfare science has become an essential field for maintaining socially responsible, ethical, and sustainable industry practice. Like traditional livestock industries, the IAFF industry could also benefit – ethically, socially, and economically – from a field of welfare science. Here, we present three economic reasons for considering animal welfare in intensive production systems: (1) improving production outcomes, (2) maintaining social license to operate, and (3) differentiating products. In each case, we provide examples from established livestock industries that highlight how the field of animal welfare science can benefit producers. Further, we provide examples of how the IAFF industry would benefit from the support of a dedicated field of welfare science. We end by calling attention to key partnerships between entomologists, welfare scientists, and producers that could advance the common goals of these stakeholder groups, as well as animal welfare in insect agriculture.