bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms
Authors: Euclide Peter T. , Larson Wesley A. , Shi Yue , Gruenthal Kristen , Christensen Kris A. , Seeb Jim , Seeb Lisa 
Published: September 2023

AbstractLocal adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. The mechanisms that create and maintain these islands and how they contribute to adaptive divergence is an active research topic. Here, we use sockeye salmon as a model to investigate both the mechanisms responsible for creating islands of divergence and the patterns of differentiation at these islands. Previous research suggested that multiple islands contributed to adaptive radiation of sockeye salmon. However, the low‐density genomic methods used by these studies made it difficult to fully elucidate the mechanisms responsible for islands and connect genotypes to adaptive variation. We used whole genome resequencing to genotype millions of loci to investigate patterns of genetic variation at islands and the mechanisms that potentially created them. We discovered 64 islands, including 16 clustered in four genomic regions shared between two isolated populations. Characterisation of these four regions suggested that three were likely created by structural variation, while one was created by processes not involving structural variation. All four regions were small (< 600 kb), suggesting low recombination regions do not have to span megabases to be important for adaptive divergence. Differentiation at islands was not consistently associated with established population attributes. In sum, the landscape of adaptive divergence and the mechanisms that create it are complex; this complexity likely helps to facilitate fine‐scale local adaptation unique to each population.
Towards a topological philosophy
Authors: Skowron Bartłomiej , Kaczmarek Janusz , Wójtowicz Krzysztof 
Published: September 2023

AbstractThis article examines the use of mathematical concepts in philosophy, focusing on topology, which may be viewed as a modern supplement to geometry. We show that Plato and Parmenides were already employing geometric ideas in their research, and discuss three examples of the application of topology to philosophical problems: the first concerns the analysis of the Cartesian distinction between res extensa and res cogitans, the second the ontology of possible worlds of Wittgenstein's Tractatus, and the third Leibniz's monadology. We also consider the role of topology in mathematical explanations of the sort found in science, arguing that it can perform a role in philosophy that is of comparable importance.
PEP444c encoded within the MIR444c gene regulates microRNA444c accumulation in barley
Authors: Chojnacka Aleksandra , Smoczynska Aleksandra , Bielewicz Dawid , Pacak Andrzej , Hensel Goetz , Kumlehn Jochen , Maciej Karlowski Wojciech , Grabsztunowicz Magda , Sobieszczuk‐Nowicka Ewa , Jarmolowski Artur , Szweykowska‐Kulinska Zofia 
Published: September 2023

AbstractMicroRNAs are small, noncoding RNA molecules that regulate the expression of their target genes. The MIR444 gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS‐box transcription factors in rice and barley. We identified three barley MIR444 (MIR444a/b/c) genes and comprehensively characterised their structure and the processing pattern of the primary transcripts (pri‐miRNAs444). Pri‐microRNAs444 undergo extensive alternative splicing, generating functional and nonfunctional pri‐miRNA444 isoforms. We show that barley pri‐miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a within MIR444a and PEP444c within MIR444c are expressed in barley plants. Moreover, we demonstrate that CRISPR‐associated endonuclease 9 (Cas9)‐mediated mutagenesis of the PEP444c‐encoding sequence results in a decreased level of PEP444 transcript in barley shoots and roots and a 5‐fold reduced level of mature microRNA444c in roots. Our observations suggest that PEP444c encoded by the MIR444c gene is involved in microRNA444c biogenesis in barley.
Local well‐posedness of the higher‐order nonlinear Schrödinger equation on the half‐line: Single‐boundary condition case
Authors: Alkın Aykut , Mantzavinos Dionyssios , Özsarı Türker 
Published: September 2023

AbstractWe establish local well‐posedness in the sense of Hadamard for a certain third‐order nonlinear Schrödinger equation with a multiterm linear part and a general power nonlinearity, known as higher‐order nonlinear Schrödinger equation, formulated on the half‐line . We consider the scenario of associated coefficients such that only one boundary condition is required and hence assume a general nonhomogeneous boundary datum of Dirichlet type at . Our functional framework centers around fractional Sobolev spaces with respect to the spatial variable. We treat both high regularity () and low regularity () solutions: in the former setting, the relevant nonlinearity can be handled via the Banach algebra property; in the latter setting, however, this is no longer the case and, instead, delicate Strichartz estimates must be established. This task is especially challenging in the framework of nonhomogeneous initial‐boundary value problems, as it involves proving boundary‐type Strichartz estimates that are not common in the study of Cauchy (initial value) problems. The linear analysis, which forms the core of this work, crucially relies on a weak solution formulation defined through the novel solution formulae obtained via the Fokas method (also known as the unified transform) for the associated forced linear problem. In this connection, we note that the higher‐order Schrödinger equation comes with an increased level of difficulty due to the presence of more than one spatial derivatives in the linear part of the equation. This feature manifests itself via several complications throughout the analysis, including (i) analyticity issues related to complex square roots, which require careful treatment of branch cuts and deformations of integration contours; (ii) singularities that emerge upon changes of variables in the Fourier analysis arguments; and (iii) complicated oscillatory kernels in the weak solution formula for the linear initial‐boundary value problem, which require a subtle analysis of the dispersion in terms of the regularity of the boundary data. The present work provides a first, complete treatment via the Fokas method of a nonhomogeneous initial‐boundary value problem for a partial differential equation associated with a multiterm linear differential operator.
A narrative analysis of clerkship reflections: Medical student identity development in a changing world
Authors: Talib Mahino A. , Greene Richard E. , Winkel Abigail Ford 
Published: September 2023

AbstractBackgroundMedical students' written reflections on their clinical experiences can be a useful tool for processing complex aspects of development as physicians. To create educational programs that scaffold adaptive professional identity development, it is essential to understand how medical students develop as professionals and process the dynamic sociocultural experiences of the current moment.ObjectiveTo explore the developing professional consciousness of medical students through clerkship reflections.DesignNarrative analysis of written reflections are produced by clerkship students, who were asked to tell a story that resonated with the physician's relationship with patient, self and colleagues. Two independent readers applied inductive labels to generate a homogenous codebook, which was used to generate themes that were then used to construct a conceptual model.Key ResultsFour themes were identified in the data that describe relationships between medical students' developing professional identities and the norms of their future professional and personal communities. These included: medical students as outsiders, conflict between the student identifying with the patient versus the healthcare team, medical students' own value judgements and, finally, the changing societal mores as they relate to social and racial injustice. The conceptual model for this experience depicts the medical student as pulled between patients and the social context on one side and the professional context of the medical centre on the other. Students long to move towards identification with the healthcare team, but reject the extremes of medical culture that they view on conflict with social and racial justice.ConclusionsMedical students in clinical training identify strongly with both patients and the medical team. Rather than viewing professional identity development as a longitudinal journey from one extreme to another, students have the power to call attention to entrenched problems within medical culture and increase empathy for patients by retaining their strong identification with the important issues of this time.
Associated criteria used in investigating suspected septic transfusion reactions: A scoping review
Authors: Acharya Dilaram , Gaussen Amaury , Poder Thomas G. , Lambert Gilles , Renaud Christian , Nawej Karlitaj , Lewin Antoine 
Published: September 2023

AbstractBackground and ObjectivesSeptic transfusion reactions (STRs) occur as a result of bacterial contamination of blood or blood products, resulting in sepsis. This scoping review aimed to identify, explore and map the available literature on the STR criteria triggering the investigation of STR.Materials and MethodsFour electronic databases (MEDLINE, Web of Science, Science Direct, Embase) were searched to retrieve scientific literature reporting such criteria, published from 1 January 2000 to 5 May 2022. Grey literature was also searched from open web sources.ResultsOf 1052 references identified, 43 (21 peer‐reviewed and 22 grey literature) met the eligibility criteria for inclusion and data extraction after full article screening. Of them, most (27/43, 62.79%) were found to report a single set of criteria, and only two reported four or more sets of criteria. The analysis of 66 sets of criteria collected from the selected references revealed 57 different sets. A few sets of criteria used only one sign and symptom (s/s) (12.12%, n = 8), whereas 16 sets used 7–15 s/s (n = 16/66; 24.24%). Of the total 319 occurrences of s/s associated with the 66 sets of criteria, post‐transfusion hyperthermia, body temperature increase and hypotension were the most common s/s categories. Of all the literature available, only one study tested the diagnostic accuracy of the STR criteria.ConclusionThis scoping review revealed a substantial variation in criteria used to identify suspected STR. Consequently, conducting further studies to enhance the diagnostic accuracy of these criteria, which trigger STR investigations, is imperative for advancing clinical practice.
Modeling human anti‐pig xenoimmune responses in a pig artery tissue grafted humanized mouse model
Authors: Fang Minghui , Zou Jun , Xu Fei , Wang Xue , Hua Shucheng , Zhou Qi , Yang Yong‐guang , Hu Zheng 
Published: September 2023

AbstractBackgroundBlood vessels that contain endothelial cells (ECs) on the surface are in direct contact with host blood and are the first target of xenograft rejection. Currently, our understanding of human anti‐pig vessel immune responses is primarily based on in vitro assays using pig ECs. Therefore, it is necessary to develop an animal model that permits in vivo study of human immunological rejection of pig vessels.MethodsPig artery tissues (PAT) were transplanted into human immune system (HIS) mice or immunodeficient NSG mice (as controls). Intragraft human immune cell infiltration and antibody deposition were quantified using histology and immunohistochemistry. Donor antigen‐specific immune responses were quantified using a mixed lymphocyte reaction and a complement‐dependent killing assay.ResultsPig CD31+ ECs were detected and increased 2‐fold from weeks 3 to 5 in PAT xenografts from immunodeficient NSG mice. However, compared with NSG mice, PAT xenografts in HIS mice had significantly lower numbers of porcine CD31+ ECs and showed a marked reduction from week 3 to week 5. PAT xenograft rejection in HIS mice is associated with intensive infiltration of human immune cells, deposition of human IgM and IgG antibodies, and the formation of a tertiary lymphoid structure. Robust donor pig antigen‐specific human T cells and antibody responses were detected in PAT‐transplanted HIS mice.ConclusionWe have developed a humanized mouse model to evaluate human anti‐pig xenoimmune responses by PAT transplantation in vivo. This model is expected to facilitate the refinement of pig gene‐editing strategies (the expression on EC surface) and the testing of local immunosuppressive strategies for clinical pig organ xenotransplantation.
Extreme values of derivatives of zeta and L‐functions
Authors: Yang Daodao 
Published: September 2023

AbstractIt is proved that as , uniformly for all positive integers , we have
where . Here, is the Dickman function. We have and when , which significantly improves previous results in [17, 40]. Similar results are established for Dirichlet L‐functions. On the other hand, when assuming the Riemann hypothesis and the generalized Riemann hypothesis, we establish upper bounds for and . Furthermore, when assuming the Granville–Soundararajan conjecture is true, we establish the following asymptotic formulas:
where is prime and is given.
Plasma measurements of the dual sugar test reveal carbohydrate immediately alleviates intestinal permeability caused by exertional heat stress
Authors: Houghton Michael J. , Snipe Rhiannon M. J. , Williamson Gary , Costa Ricardo J. S. 
Published: September 2023

AbstractThe aim of this set of randomised cross‐over studies was to determine the impact of progressive heat exposure and carbohydrate or protein feeding during exertional stress on small intestine permeability using a dual sugar test. In our previous work, and typically in the field, recovery of lactulose and l‐rhamnose is measured cumulatively in urine. This follow‐up study exploits our novel high‐performance anion exchange chromatography with pulsed amperometric detection (HPAEC‐PAD) protocol to accurately quantify the sugars in plasma. Endurance‐trained participants completed experimental trial A (ET‐A; n = 8), consisting of 2 h running at 60% in temperate, warm and hot ambient conditions, and/or experimental trial B (ET‐B; n = 9), consisting of 2 h running at 60% in the heat while consuming water, carbohydrate or protein. Blood samples were collected and plasma lactulose (L) and l‐rhamnose (R) appearance, after dual sugar solution ingestion at 90 min of exercise, was quantified by HPAEC‐PAD to measure plasma L/R and reveal new information about intestinal permeability immediately post‐exercise and during recovery. In ET‐A, plasma L/R increased immediately post‐exercise in hot compared with temperate and warm conditions, while, in ET‐B, carbohydrate alleviated this, and this information was otherwise missed when measuring urine L/R. Consuming carbohydrate or protein before and during exercise attenuated small intestine permeability throughout recovery from exertional heat stress. We recommend using the dual sugar test with quantification of plasma sugars by HPAEC‐PAD at intervals to maximise intestinal permeability data collection in exercise gastroenterology research, as this gives additional information compared to urinary measurements.
imageKey points
Intestinal permeability is typically assessed using a dual sugar test, by administering a drink containing non‐metabolisable sugars (e.g. lactulose (L) and l‐rhamnose (R)) that can enter the circulation by paracellular translocation when the epithelium is compromised, and are subsequently measured in urine.
We demonstrate that our recently developed ion chromatography protocol can be used to accurately quantify the L/R ratio in plasma, and that measuring L/R in plasma collected at intervals during the post‐exercise recovery period reveals novel acute response information compared to measuring 5‐h cumulative urine L/R.
We confirm that exercising in hot ambient conditions increases intestinal epithelial permeability immediately after exercise, while consuming carbohydrate or protein immediately before and during exercise attenuates this.
We recommend using our dual sugar absorption test protocol to maximise intestinal epithelial permeability data collection in exercise gastroenterology research and beyond.
Large-scale genomic survey and characterization of mcr genes carried by foodborne
Cronobacter
isolates
Authors: Zhu Qianhui , Hu Jinrui , Liu Na , Qi Heyuan , Du Xiaoli , Cui Zhigang , Sun Yan , Liu Yadong , Hu Songnian , Wu Linhuan , Zhou Haijian , He Zilong , Ma Juncai 
Published: September 2023

ABSTRACT

Antibiotic resistance has become a worldwide public health and biosafety problem. The clinical efficacy of colistin was jeopardized by the report of the first mobile colistin resistance (mcr) gene, and subsequently, the mcr-gene family of mcr-1 to mcr-10 has been identified.
Cronobacter
is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and necrotizing enterocolitis (NEC) by contaminating food. However, the entire picture of foodborne
Cronobacter
carriage of the mcr genes is not known. Here, we investigated the mcr genes of
Cronobacter
isolates (
N
= 877) by whole-genome sequencing. We found 133 of 877 previously undescribed
Cronobacter
isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne
Cronobacter
isolates, and the flanking structure carrying IS1R was found for the first time in this study. These findings suggest that foodborne
Cronobacter
isolates carrying the mcr genes already pose a threat to human health.

IMPORTANCE

Cronobacter
is an emerging foodborne opportunistic pathogen, which can cause neonatal meningitis, bacteremia, and NEC by contaminating food. However, the entire picture of foodborne
Cronobacter
carriage of the mcr genes is not known. Here, we investigated the mcr genes of
Cronobacter
isolates by whole-genome sequencing and found 133 previously undescribed
Cronobacter
isolates carrying mcr genes. Further genomic analysis revealed that these mcr genes mainly belonged to the mcr-9 and mcr-10. Genomic analysis of the flanking structures of mcr genes revealed that two core flanking structures were prevalent in foodborne
Cronobacter
isolates, and the flanking structure carrying IS1R was found for the first time in this study.
Arsenic trioxide-induced apoptosis contributes to suppression of viral reservoir in SIV-infected rhesus macaques
Authors: He Yizi , Wu Chunxiu , Liu Zijian , Zhang Yudi , Feng Fengling , Lin Zihan , Wang Congcong , Yang Qing , Wen Ziyu , Liu Yichu , Zhang Fan , Lin Yanqin , Zhang Hao , Qu Linbing , Li Linghua , Cai Weiping , Sun Caijun , Chen Ling , Li Pingchao 
Published: September 2023

ABSTRACT

Latent viral reservoir is recognized as the major obstacle to achieving a functional cure for HIV infection. We previously reported that arsenic trioxide (As
2
O
3
) combined with antiretroviral therapy (ART) can reactivate the viral reservoir and delay viral rebound after ART interruption in chronically simian immunodeficiency virus (SIV)-infected macaques. In this study, we further investigated the effect of As
2
O
3
independent of ART in chronically SIV-infected macaques. We found that As
2
O
3
-only treatment significantly increased the CD4/CD8 ratio, improved SIV-specific T cell responses, and reactivated viral latency in chronically SIVmac239-infected macaques. RNA-sequencing analysis revealed that As
2
O
3
treatment downregulated the expression levels of genes related to HIV entry and infection, while the expression levels of genes related to transcription initiation, cell apoptosis, and host restriction factors were significantly upregulated. Importantly, we found that As
2
O
3
treatment specifically induced apoptosis of SIV-infected CD4
+
T cells. These findings revealed that As
2
O
3
might not only impact viral latency, but also induce the apoptosis of HIV-infected cells and thus block the secondary infection of bystanders. Moreover, we investigated the therapeutic potential of this regimen in acutely SIVmac239-infected macaques and found that As
2
O
3
+ ART treatment effectively restored the CD4
+
T cell count, delayed disease progression, and improved survival in acutely SIV-infected macaques. In sum, this work provides new insights to develop As
2
O
3
as a component of the “shock-and-kill” strategy toward HIV functional cure.

IMPORTANCE

Although antiretroviral therapy (ART) can effectively suppress the viral load of AIDS patients, it cannot functionally cure HIV infection due to the existence of HIV reservoir. Strategies toward HIV functional cure are still highly anticipated to ultimately end the pandemic of AIDS. Herein, we investigated the direct role of As
2
O
3
independent of ART in chronically SIV-infected macaques and explored the underlying mechanisms of the potential of As
2
O
3
in the treatment of HIV/SIV infection. Meanwhile, we investigated the therapeutic effects of ART+As
2
O
3
in acutely SIVmac239-infected macaques. This study showed that As
2
O
3
has the potential to be launched into the “shock-and-kill” strategy to suppress HIV/SIV reservoir due to its latency-reversing and apoptosis-inducing properties.
Energy of Tornadoes and Landspouts
Authors: Golitsyn G. S. , Chernokulsky A. V. , Vazaeva N. V. 
Published: September 2023

Abstract
According to the data on the sizes and intensity of tornadoes and landspouts, their characteristic times and forcings are found. Depending on the intensity, the average times vary by a factor of three and the forcings by a factor of six. The energy of the vortices is estimated and is expressed, among other things, in TNT equivalent mass units.
New Data on Geology and Paleogeographical Evolution of the Southern East Siberian Sea in the Quaternary
Authors: Petrov O. V. , Ryabchuk D. V. , Sergeev A. Yu. , Budanov L. M. , Zhamoida V. A. , Neevin I. A. , Taldenkova E. E. , Prishchepenko D. V. , Nosevich E. S. , Pushina Z. V. , Grigoriev A. G. , Bashirova L. D. , Ponomarenko E. P. 
Published: September 2023

Abstract
The paper deals with results of geological and geophysical study of the East Siberian Sea coastal areas are reported. Research activities started in 2018 in the frame of the State Geological Mapping Project (GK-1000/3) and continued in 2022 under support of the Russian Science Foundation. A seismo-stratigraphic scheme of the Quaternary sediment sequence has been compiled, and a conception of the paleogeographical evolution in the Late Pleistocene–Holocene has been proposed.
The First Discovery of Cambrian Volcanic Rocks and Plagiogranites in the Tekturmas Ophiolite Zone (Central Kazakhstan): Age and Composition
Authors: Degtyarev K. E. , Luchitskaya M. V. , Tretyakov A. A. 
Published: September 2023

Abstract
The complex of felsic to intermediate volcanic rocks intruded by plagiogranitic bodies is first revealed in the western part of the Tekturmas ophiolite zone of Central Kazakhstan. The U–Pb (SIMS) geochronological study of one of the plagiogranitic bodies dated back to the Early Cambrian (537 ± 5 Ma) is conducted for the first time. The peculiarities of the volcanic rocks and the composition of plagiogranites indicate their formation in a suprasubduction setting within the Early Cambrian primitive volcanic island arc. The formation of this arc was not related to the evolution of the Ordovician oceanic structures, the complexes of which participate in the structure of the Tekturmas zone.