bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure of bacteria–fungi bipartite networks along elevational gradients in contrasting climates
Authors: Zhao Wenqian , Soininen Janne , Hu Ang , Liu Jinfu , Li Mingjia , Wang Jianjun 
Published: July 2024

AbstractClimate change is altering species distribution and modifying interactions in microbial communities. Understanding microbial community structure and their interactions is crucial to interpreting ecosystem responses to climate change. Here, we examined the assemblages of stream bacteria and fungi, and the associations between the two groups along elevational gradients in two regions with contrasting precipitation and temperature, that is the Galong and Qilian mountains of the Tibetan Plateau. In the wetter and warmer region, the species richness significantly increased and decreased with elevation for bacteria and fungi, respectively, while were nonsignificant in the drier and colder region. Their bipartite network structure was also different by showing significant increases in connectance and nestedness towards higher elevations only in the wetter and warmer region. In addition, these correlation network structure generally exhibited similar positive association with species richness in the wetter and warmer region and the drier and colder region. In the wetter and warmer region, climatic change along elevation was more important in determining connectance and nestedness, whereas microbial species richness exerted a stronger influence on network structure and robustness in the drier and colder region. These findings indicate substantial forthcoming changes in microbial diversity and network structure in warming climates, especially in wetter and warmer regions on Earth, advancing the understanding of microbial bipartite interactions' response to climate change.
Fluid‐Dynamic Modeling of Flow in Embryonic Tissue Indicates That Lymphatic Valve Location Is Not Consistently Determined by the Local Fluid Shear or Its Gradient
Authors: Bertram Christopher D. , Macaskill Charlie 
Published: July 2024

ABSTRACTObjectiveIntravascular lymphatic valves often occur in proximity to vessel junctions. It is commonly held that disturbed flow at junctions is responsible for accumulation of valve‐forming cells (VFCs) at these locations as the initial step in valve creation, and the one which explains the association with these sites. However, evidence in favor is largely limited to cell culture experiments.MethodsWe acquired images of embryonic lymphatic vascular networks from day E16.5, when VFC accumulation has started but the developing valve has not yet altered the local vessel geometry, stained for Prox1, which co‐localizes with Foxc2. Using finite‐element computational fluid mechanics, we simulated the flow through the networks, under conditions appropriate to this early development stage. Then we correlated the Prox1 distributions with the distributions of simulated fluid shear and shear stress gradient.ResultsAcross a total of 16 image sets, no consistent correlation was found between Prox1 distribution and the local magnitude of fluid shear, or its positive or negative gradient.ConclusionsThis, the first direct semi‐empirical test of the localization hypothesis to interrogate the tissue from in vivo at the critical moment of development, does not support the idea that a feature of the local flow determines valve localization.
Arithmetical pluralism and the objectivity of syntax
Authors: Picollo Lavinia , Waxman Daniel 
Published: July 2024

AbstractArithmetical pluralism is the view that there is not one true arithmetic but rather many apparently conflicting arithmetical theories, each true in its own language. While pluralism has recently attracted considerable interest, it has also faced significant criticism. One powerful objection, which can be extracted from Parsons (2008), appeals to a categoricity result to argue against the possibility of seemingly conflicting true arithmetics. Another salient objection raised by Putnam (1994) and Koellner (2009) draws upon the arithmetization of syntax to argue that arithmetical pluralism is inconsistent with the objectivity of syntax. First, we review these arguments and explain why they ultimately fail. We then offer a novel, more sophisticated argument that avoids the pitfalls of both. Our argument combines strategies from both objections to show that pluralism about arithmetic entails pluralism about syntax. Finally, we explore the viability of pluralism in light of our argument and conclude that a stable pluralist position is coherent. This position allows for the possibility of rival packages of arithmetic and syntax theories, provided that they systematically co‐vary with one another.
ArabidopsisPROTODERMAL FACTOR2 binds lysophosphatidylcholines and transcriptionally regulates phospholipid metabolism
Authors: Wojciechowska Izabela , Mukherjee Thiya , Knox‐Brown Patrick , Hu Xueyun , Khosla Aashima , Subedi Bibek , Ahmad Bilal , Mathews Graham L. , Panagakis Ashley A. , Thompson Kyle A. , Peery Sophie T. , Szlachetko Jagoda , Thalhammer Anja , Hincha Dirk K. , Skirycz Aleksandra , Schrick Kathrin 
Published: July 2024

Summary

Plant homeodomain leucine zipper IV (HD‐Zip IV) transcription factors (TFs) contain an evolutionarily conserved steroidogenic acute regulatory protein (StAR)‐related lipid transfer (START) domain. While the START domain is required for TF activity, its presumed role as a lipid sensor is not clear.

Here we used tandem affinity purification from Arabidopsis cell cultures to demonstrate that PROTODERMAL FACTOR2 (PDF2), a representative member that controls epidermal differentiation, recruits lysophosphatidylcholines (LysoPCs) in a START‐dependent manner. Microscale thermophoresis assays confirmed that a missense mutation in a predicted ligand contact site reduces lysophospholipid binding.

We additionally found that PDF2 acts as a transcriptional regulator of phospholipid‐ and phosphate (Pi) starvation‐related genes and binds to a palindromic octamer with consensus to a Pi response element. Phospholipid homeostasis and elongation growth were altered in pdf2 mutants according to Pi availability. Cycloheximide chase experiments revealed a role for START in maintaining protein levels, and Pi starvation resulted in enhanced protein destabilization, suggesting a mechanism by which lipid binding controls TF activity.

We propose that the START domain serves as a molecular sensor for membrane phospholipid status in the epidermis. Our data provide insights toward understanding how the lipid metabolome integrates Pi availability with gene expression.
Identification of schizophrenia by applying interpretable radiomics modeling with structural magnetic resonance imaging of the cerebellum
Authors: Bang Minji , Park Kisung , Choi Seoung‐Ho , Ahn Sung Soo , Kim Jinna , Lee Seung‐Koo , Park Yae Won , Lee Sang‐Hyuk 
Published: July 2024

AimsThe cerebellum is involved in higher‐order mental processing as well as sensorimotor functions. Although structural abnormalities in the cerebellum have been demonstrated in schizophrenia, neuroimaging techniques are not yet applicable to identify them given the lack of biomarkers. We aimed to develop a robust diagnostic model for schizophrenia using radiomic features from T1‐weighted magnetic resonance imaging (T1‐MRI) of the cerebellum.MethodsA total of 336 participants (174 schizophrenia; 162 healthy controls [HCs]) were allocated to training (122 schizophrenia; 115 HCs) and test (52 schizophrenia; 47 HCs) cohorts. We obtained 2568 radiomic features from T1‐MRI of the cerebellar subregions. After feature selection, a light gradient boosting machine classifier was trained. The discrimination and calibration of the model were evaluated. SHapley Additive exPlanations (SHAP) was applied to determine model interpretability.ResultsWe identified 17 radiomic features to differentiate participants with schizophrenia from HCs. In the test cohort, the radiomics model had an area under the curve, accuracy, sensitivity, and specificity of 0.89 (95% confidence interval: 0.82–0.95), 78.8%, 88.5%, and 75.4%, respectively. The model explanation by SHAP suggested that the second‐order size zone non‐uniformity feature from the right lobule IX and first‐order energy feature from the right lobules V and VI were highly associated with the risk of schizophrenia.ConclusionThe radiomics model focused on the cerebellum demonstrates robustness in diagnosing schizophrenia. Our results suggest that microcircuit disruption in the posterior cerebellum is a disease‐defining feature of schizophrenia, and radiomics modeling has potential for supporting biomarker‐based decision‐making in clinical practice.
Radiographic assessment of the peri‐implant site
Authors: Sahrmann Philipp , Kühl Sebastian , Dagassan‐Berndt Dorothea , Bornstein Michael M. , Zitzmann Nicola U. 
Published: July 2024

AbstractWhile peri‐implant mucositis relies solely on clinical parameters, radiological assessment becomes indispensable for diagnosing peri‐implantitis. Intraoral radiography, with its simplicity of application, low radiation exposure, and adequate representation of peri‐implant structures, stands out as the standard of care for both immediate and follow‐up assessments. Standardization by custom‐made radiologic splints allows for excellent comparability with previous images and allows for the determination of even small changes in contour and density of the peri‐implant bone. Furthermore, other radiographic modalities like panoramic radiography and cone beam computed tomography (CBCT) may provide useful features for specific patients and clinical cases while also showing innate limitations. Beyond the assessment of the marginal peri‐implant bone level as the crucial parameter of clinical relevance, radiologic assessment may reveal various other findings related to the prosthetic restoration itself, the precision of its fit to the implant, and the peri‐implant soft and hard tissues. Since such findings can be crucial for the assessment of peri‐implant health and the implants' prognosis, a systematic diagnostic evaluation pathway for a thorough assessment is recommended to extract all relevant information from radiologic imaging. This article also provides an overview of the clinical and chronological indications for different imaging modalities in peri‐implant issues.
External skeletal fixation for the treatment of pelvic fractures in cats
Authors: Fitzpatrick Noel , Guthrie James W. , Hamilton Michael H. 
Published: July 2024

AbstractObjectiveTo report the technique and the outcome for the repair of pelvic fractures in cats using external skeletal fixation (ESF).Study designRetrospective case series.AnimalsClient‐owned cats (n = 125).MethodsMedical records of cats with pelvic fractures, treated with an ESF between June 2001 and June 2009, were reviewed. Preoperative, immediate postoperative, and more than 4 weeks’ postoperative radiographs were compared. Clinical examination was performed 4 to 9 weeks following surgery. Longer term follow up (4 to 80 months) was conducted by client questionnaire.ResultsNo intraoperative complications occurred. There was no change in the pelvic canal width observed on follow‐up radiographs (p = .16). Implant loosening was noted on follow‐up radiographs in 16/125 (13%) of cases, and 67/803 (8%) pins were palpably loose at the time of frame removal. The mean time to frame removal was 37 ± 9 days. No long‐term complications were reported. Long‐term mean mobility score was 95 ± 5 and median lameness was 0 (range: 0–2).ConclusionAn ESF may be successfully applied for the stabilization of various pelvic fractures in cats.Clinical significanceThe application of an ESF for the management of pelvic fractures in cats provides good outcomes.
Leveraging biotin-based proximity labeling to identify cellular factors governing early alphaherpesvirus infection
Authors: Quan Jenai , Fan Qing , Simons Lacy M. , Smukowski Samuel N. , Pegg Caitlin , Longnecker Richard , Savas Jeffrey N. , Hultquist Judd F. , Smith Gregory A. 
Published: July 2024

ABSTRACT

Neurotropic alphaherpesviruses, including herpes simplex virus type 1 and pseudorabies virus, establish a lifelong presence within the peripheral nervous system of their mammalian hosts. Upon entering cells, two conserved tegument proteins, pUL36 and pUL37, traffic DNA-containing capsids to nuclei. These proteins support long-distance retrograde axonal transport and invasion of the nervous system
in vivo
. To better understand how pUL36 and pUL37 function, recombinant viral particles carrying BioID2 fused to these proteins were produced to biotinylate cellular proteins in their proximity (<10 nm) during infection. Eighty-six high-confidence host proteins were identified by mass spectrometry and subsequently targeted by CRISPR-Cas9 gene editing to assess their contributions to early infection. Proteins were identified that both supported and antagonized infection in immortalized human epithelial cells. The latter included zyxin, a protein that localizes to focal adhesions and regulates actin cytoskeletal dynamics. Zyxin knockout cells were hyper-permissive to infection and could be rescued with even modest expression of GFP-zyxin. These results provide a resource for studies of the virus-cell interface and identify zyxin as a novel deterrent to alphaherpesvirus infection.

IMPORTANCE
Neuroinvasive alphaherpesviruses are highly prevalent with many members found across mammals [e.g., herpes simplex virus type 1 (HSV-1) in humans and pseudorabies virus in pigs]. HSV-1 causes a range of clinical manifestations from cold sores to blindness and encephalitis. There are no vaccines or curative therapies available for HSV-1. A fundamental feature of these viruses is their establishment of lifelong infection of the nervous system in their respective hosts. This outcome is possible due to a potent neuroinvasive property that is coordinated by two proteins: pUL36 and pUL37. In this study, we explore the cellular protein network in proximity to pUL36 and pUL37 during infection and examine the impact of knocking down the expression of these proteins upon infection.
Butyrate promotes visceral hypersensitivity in IBS model via mast cell-derived DRG neuron lincRNA-01028-PKC-TRPV1 pathway
Authors: Li Ying-Jie , Li Jing , Dai Cong 
Published: July 2024

ABSTRACT

Emerging evidence indicates that gut dysbiosis is involved in the pathogenesis of visceral hypersensitivity (VH). However, how gut microbiota contributes to the development of VH is unknown. Here, we sought to examine the signal transduction pathways from gut to dorsal root ganglion (DRG) responsible for this. Therefore, abdominal withdrawal reflex (AWR) scores, fecal output, fecal water content, and total gastrointestinal transit time (TGITT) were assessed in Con rats, VH rats, rats treated with NaB, and VH rats treated with VSL#3. Fecal microbiota and its metabolite (short-chain fatty acids, SCFAs), mast cell degranulation in colon, lincRNA-01028, miR-143, and protease kinase C (PKC) and TRPV1 expression in DRGs were further detected. VH rats showed an increased fecal water content, a shortened TGITT, an increased abundance of Clostridium
sensu stricto
1 and increased butyrate in fecal samples, an increased mast cell degranulation, an increased expression of lincRNA-01028, PKC, and TRPV1, and a decreased expression of miR-143 in DRGs compared with control rats, which could be restored by the application of probiotic VSL#3. The above-mentioned detection in rats treated with butyrate was similar to that of VH rats. We further confirm whether butyrate sensitized DRG neurons by a lincRNA-01028, miR-143, and PKC-dependent mechanism via mast cell
in vitro
. In co-cultures, MCs treated with butyrate elicited a higher TRPV1 current, a higher expression of lincRNA-01028, PKC, and a lower expression of miR-143 in DRG neurons, which could be inhibited by a lincRNA-01028 inhibitor. These findings indicate that butyrate promotes visceral hypersensitivity via mast cell-derived DRG neuron lincRNA-01028-PKC-TRPV1 pathway.

IMPORTANCE

Irritable bowel syndrome (IBS), characterized by visceral hypersensitivity, is a common gastrointestinal dysfunction syndrome. Although the gut microbiota plays a role in the pathogenesis and treatment of irritable bowel syndrome (IBS), the possible underlying mechanisms are unclear. Therefore, it is of critical importance to determine the signal transduction pathways from gut to DRG responsible for this
in vitro
and
in vivo
assay. This study demonstrated that butyrate sensitized TRPV1 in DRG neurons via mast cells
in vivo
and
in vitro
by a lincRNA-01028, miR-143, and PKC-dependent mechanism. VH rats similarly showed an increased abundance of Clostridium
sensu stricto
1, an increased fecal butyrate, an increased mast cell degranulation, and increased expression of TRPV1 compared with control rats, which could be restored by the application of VSL#3. In conclusion, butyrate produced by the altered intestinal microbiota is associated with increased VH.
Variations in candidalysin amino acid sequence influence toxicity and host responses
Authors: Wickramasinghe Don N. , Lyon Claire M. , Lee Sejeong , Hepworth Olivia W. , Priest Emily L. , Maufrais Corinne , Ryan Adam P. , Permal Emmanuelle , Sullivan Derek , McManus Brenda A. , Hube Bernhard , Butler Geraldine , d'Enfert Christophe , Naglik Julian R. , Richardson Jonathan P. 
Published: July 2024

ABSTRACT

Candida albicans
causes millions of mucosal infections in humans annually. Hyphal overgrowth on mucosal surfaces is frequently associated with tissue damage caused by candidalysin, a secreted peptide toxin that destabilizes the plasma membrane of host cells thereby promoting disease and immunopathology. Candidalysin was first identified in
C. albicans
strain SC5314, but recent investigations have revealed candidalysin “variants” of differing amino acid sequence in isolates of
C. albicans
, and the related species
C. dubliniensis
, and
C tropicalis
, suggesting that sequence variation among candidalysins may be widespread in natural populations of these
Candida
species. Here, we analyzed
ECE1
gene sequences from 182
C
.
albicans
isolates, 10
C
.
dubliniensis
isolates, and 78
C
.
tropicalis
isolates and identified 10, 3, and 2 candidalysin variants in these species, respectively. Application of candidalysin variants to epithelial cells revealed differences in the ability to cause cellular damage, changes in metabolic activity, calcium influx, MAPK signalling, and cytokine secretion, while biophysical analyses indicated that variants exhibited differences in their ability to interact with and permeabilize a membrane. This study identifies candidalysin variants with differences in biological activity that are present in medically relevant
Candida
species.

IMPORTANCE

Fungal infections are a significant burden to health. Candidalysin is a toxin produced by
Candida albicans
that damages host tissues, facilitating infection. Previously, we demonstrated that candidalysins exist in the related species
C. dubliniensis
and
C. tropicalis
, thereby identifying these molecules as a toxin family. Recent genomic analyses have highlighted the presence of a small number of candidalysin “variant” toxins, which have different amino acid sequences to those originally identified. Here, we screened genome sequences of isolates of
C. albicans
,
C. dubliniensis
, and
C. tropicalis
and identified candidalysin variants in all three species. When applied to epithelial cells, candidalysin variants differed in their ability to cause damage, activate intracellular signaling pathways, and induce innate immune responses, while biophysical analysis revealed differences in the ability of candidalysin variants to interact with lipid bilayers. These findings suggest that intraspecies variation in candidalysin amino acid sequence may influence fungal pathogenicity.
Genome sequences of three
Bartonella schoenbuchensis
strains from Czechia
Authors: Solis Cayo Luis , Hammerbauerová Iva , Sommer Julian , Nemati Zahra , Ballhorn Wibke , Tsukayama Pablo , Dichter Alexander , Votýpka Jan , Kempf Volkhard A. J. 
Published: July 2024

ABSTRACT

Bartonella schoenbuchensis
causes bacteremia in ruminants and is transmitted by deer keds. Here, we report the complete genome sequences of three
B. schoenbuchensis strains
(L2, L19, and L24) recently isolated from deer keds (
Lipoptena fortisetosa
) in Czechia.
Hospital mortality and length of stay associated with
Enterobacterales
positive blood cultures: a multicenter analysis
Authors: Cooper Lauren , Yu Kalvin , Van Benten Kayla , Patkar Anuprita , Ye Gang , Gregory Sara , Ai ChinEn , Gupta Vikas 
Published: July 2024

ABSTRACT

Delayed time to antimicrobial susceptibility results can impact patients’ outcomes. Our study evaluated the impact of susceptibility turnaround time (TAT) and inadequate empiric antibacterial therapy (IET) in patients with bloodstream infections (BSI) caused by
Enterobacterales
(ENT) species on in-hospital mortality and length of stay (LOS). This retrospective, multicenter investigation which included 29,570 blood ENT-positive admissions across 161 US healthcare facilities evaluated the association between antimicrobial susceptibility testing (AST) TAT, carbapenem susceptibility, and empiric therapy on post-BSI in-hospital mortality and LOS following an ENT BSI event in adult patients. After adjusting for outcomes covariates, post-BSI in-hospital mortality was significantly higher for patients in the IET vs adequate empiric therapy (AET) group [odds ratio (OR): 1.61 (95% CI: 1.32, 1.98);
P
< 0.0001], and when AST TAT was >63 h [OR:1.48 (95% CI: 1.16, 1.90);
P
= 0.0017]. Patients with carbapenem non-susceptible (carb-NS) ENT BSI had significantly higher LOS (16.6 days, 95% CI: 15.6, 17.8) compared to carbapenem susceptible (carb-S, 12.2 days, 95% CI: 11.8, 12.6), (
P
< 0.0001). Extended AST TAT was significantly associated with longer LOS for TAT of 57–65 h and >65 h (
P
= 0.005 and
P
< 0.0001, respectively) compared to TAT ≤42 h (reference). Inadequate empiric therapy (IET), carb-NS, and delayed AST TAT are significantly associated with adverse hospital outcomes in ENT BSI. Workflows that accelerate AST TAT for ENT BSIs and facilitate timely and adequate therapy may reduce post-BSI in-hospital mortality rate and LOS.

IMPORTANCE

For patients diagnosed with bloodstream infections (BSI) caused by
Enterobacterales
(ENT), delayed time to antimicrobial susceptibility (AST) results can significantly impact in-hospital mortality and hospital length of stay. However, this relationship between time elapsed from blood culture collection to AST results has only been assessed, to date, in a limited number of publications. Our study focuses on this important gap using retrospective data from 29,570 blood ENT-positive admissions across 161 healthcare facilities in the US as we believe that a thorough understanding of the dynamic between AST turnaround time, adequacy of empiric therapy, post-BSI event mortality, and hospital length of stay will help guide effective clinical management and optimize outcomes of patients with ENT infections.
Supplemental Material: Upper Paleozoic komatiites near Mashhad, NE Iran
Authors: Mobasheri Mohsen , al. et 
Published: July 2024

<p> S1—a description of the contents of an article in preparation; S2—analytical methods; Table S1—compositions of olivine; Table S2—compositions of Cr spinel; Table S3—major and trace elements in samples; and Figures S1–S5.</p>