bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel approach to simultaneous genotyping of human platelet antigen systems and human leucocyte antigen class I loci using PacBio long‐read sequencing
Authors: Zhao Peizhe , Lyu Qilu , Xu Yi , Liang Yajun , Wu Yunxiang , Li Qing , Wang Hua , Yuan Yao , He Runjun , Fu Weiyi , Zhang Demei , Kong Yujie 
Published: October 2024

AbstractBackground and ObjectivesAccurate human leucocyte antigen (HLA) and human platelet antigen (HPA) typing is essential for establishing a blood platelet donor bank to deal with refractoriness in patients undergoing multiple platelet transfusions. Current methods, such as Sanger and next‐generation sequencing, encounter difficulties in haplotyping. Herein, the aim of this study was to establish a method for HLA and HPA typing based on the long read sequencing.Study Design and MethodsThe HPA and HLA class I genotypes of 268 platelet donors from the Taiyuan Blood Center, China were identified using long‐read sequencing on the PacBio platform. Allele frequencies for HPA systems and HLA class I genes were calculated, and genetic variability within HPA system genes was analysed.ResultsPolymorphisms were identified in 8 of the 35 HPA systems (HPA‐1 to HPA‐6w, HPA‐15 and HPA‐21w), with the frequencies of the ‘b’ allele at 0.0187, 0.0709, 0.4086, 0.0075, 0.0149, 0.0317, 0.4310 and 0.0019, respectively. The alleles with the highest frequencies at the HLA‐A, HLA‐B and HLA‐C loci are HLA‐A02:01, B51:01, B46:01 and C06:02, respectively. Additionally, several genetic patterns in HPA systems were identified, including the c.166‐1029C>T variant, which was found exclusively in samples carrying the HPA‐1b allele.ConclusionThis study developed a targeted long‐read sequencing method characterized by high throughput and simultaneity, capable of resolving allele ambiguities for effective HLA class I genotyping in establishing a platelet donor bank.
Diagnostic imaging findings in lame Warmblood horses with bone injuries of the medial proximal phalanx glenoid cavity
Authors: Vandersmissen Maxime , Evrard Laurence , Charles Alexandre , Audigié Fabrice , Busoni Valeria 
Published: October 2024

AbstractThis retrospective study aims to describe baseline and follow‐up imaging findings in subchondral and trabecular bone damage occurring outside of the sagittal groove in the proximal phalanx (P1) glenoid in a case series of lame Warmblood horses. Thirteen lame horses (16 forelimbs) with standing magnetic resonance imaging (sMRI) evidence of nonsagittal groove glenoid subchondral and trabecular bone injury of P1 as the main lesion were included. All injuries were located at the medial aspect of the P1 glenoid. At sMRI, changes included subchondral bone plate thickening and trabecular sclerosis, bone marrow edema‐like signal, subchondral bone resorption (11/16), and new bone production (8/16). Subchondral bone resorption in the transverse plane was linear (8/11), round (2/11), or ill‐defined (1/11). Sclerosis, bone resorption, and new bone production were seen radiographically in 10, 4, and 5 limbs, respectively. All limbs had concurrent metacarpal condyle sMRI imaging abnormalities, osteophytosis, and joint effusion. Follow‐up sMRIs were obtained in 8 of 16 limbs, five of which showing progression of the resorptive lesion. One horse encountered a comminuted fracture of the affected P1 18 months after the follow‐up sMRI examination. The imaging appearance of the medial glenoid bone injuries of P1 in this case series is consistent with chronic bone overload. The linear configuration of bone resorption seen in eight lesions suggests short, incomplete stress fractures, which is supported by the ultimate catastrophic fracture occurring in one case.
Characteristics of advanced practice nurses’ clinical competence in primary health care settings: a scoping review protocol
Authors: Troncoso-Valenzuela Bernardita , de Almeida Lopes Monteiro da Cruz Diná , Quiroga Toledo Natalia 
Published: October 2024

Objective:
This scoping review aims to identify the clinical competency characteristics, in terms of knowledge, skills, and attitudes, of advanced practice nurses in primary health care settings.

Introduction:
Although much has been written about the competencies of advanced practice nurses, more detail about the skills, knowledge, and attitudes that inform their clinical competence in primary health care needs to be ascertained. This will promote the development, implementation, and evaluation of advanced nursing practice in contexts where it is unavailable.

Inclusion criteria:
Studies that address the clinical competency characteristics of advanced practice nurses in primary health care settings will be considered for inclusion.

Methods:
This review will be conducted according to JBI methodology for scoping reviews. A comprehensive search will be conducted in PubMed, CINAHL (EBSCOhost), Web of Science Core Collection, Scopus, Virtual Health Library, Scientific Electronic Library Online, Embase, ScienceDirect, Cochrane Library, and Google Scholar for primary and secondary qualitative, quantitative, and mixed methods studies on the topic of relevance. Gray literature will be searched in DART-E, TESES CAPES, CAUL (Australian Digital Theses), and Theses Canada Editorials. Letters, editorials, commentaries, conference abstracts, and documents published by advanced practice nurses’ associations will also be considered for inclusion. Two independent reviewers will screen the studies at title and abstract and at full text. The same reviewers will extract relevant data using an instrument developed by the reviewers. These data will be presented in a narrative synthesis to facilitate the analysis of the evidence found.

Review registration:
Open Science Framework https://osf.io/zbqdn
Association Between Accelerometer-Measured Physical Activity and Mobility Limitations in Twins
Authors: Pullinen Pia , Parkkari Jari , Kaprio Jaakko , Vähä-Ypyä Henri , Sievänen Harri , Kujala Urho , Waller Katja 
Published: October 2024

Background: The associations between mobility limitations and device-measured physical activity are sparsely studied. In this study, these associations are studied among community-dwelling older twins. Methods: This cross-sectional study utilized data gathered in 2014–2016 for the MOBILETWIN study. Participants were twins born in Finland between 1940 and 1944 (774 participants, mean age 73 years). Physical activity was measured with a hip-worn accelerometer. Mobility limitations were assessed with a questionnaire. Results: Individual-level analyses revealed that physical activity was associated with mobility limitations. Participants with severe mobility limitations took 2,637 (SD = 1,747) steps per day, those with some mobility limitations 4,437 (SD = 2,637) steps, and those without mobility limitations 7,074 (SD = 2,931) steps (p < .05). The within-twin pair analyses revealed the same pattern for the 144 dizygotic twin pairs, but no associations were seen for the 117 monozygotic twin pairs. Conclusions: Accelerometer-measured physical activity and mobility limitations were associated in community-dwelling older adults. Genetic factors may explain some of the variations in physical activity. Significance: A personalized exercise program to promote increased physical activity should be provided for older adults who report mobility difficulties. Future research is needed to examine causality between physical activity and mobility limitations.
Screening and functional characterization of isocitrate lyase AceA in the biofilm formation of
Vibrio alginolyticus
Authors: Shi Weibo , Li Ya , Zhang Weiwei 
Published: October 2024

ABSTRACT

Biofilm is a well-known sessile lifestyle for bacterial pathogens, but a little is known about the mechanism on biofilm formation in
Vibrio alginolyticus
. In this study, we screened
V. alginolyticus
strains with strong biofilm formation ability from coastal seawater. The antibiotic resistance of the biofilm cells (BFs) was higher than that of the planktonic cells (PTs). To study the genes and pathways involved in biofilm formation, we performed transcriptome analysis of the BFs and PTs of
V. alginolyticus
R9. A total of 685 differentially expressed genes (DEGs) were upregulated, and 517 DEGs were downregulated in the BFs. The upregulated DEGs were significantly enriched in several pathways including glyoxylate and dicarboxylate metabolism, while the downregulated genes were significantly enriched in the flagellar assembly pathways. The key gene involved in glyoxylate shunt,
aceA
, was cloned, and Δ
aceA
mutant was constructed to determine the function of AceA in carbon source utilization, biofilm formation, and virulence. Real-time reverse transcription PCR showed that the expression of
aceA
was higher at the mature stage but lower at the disperse stage of biofilm formation, and the expression of the flagellar related genes was upregulated in Δ
aceA
. This is the first study to illustrate the global gene expression profile during the biofilm formation of
V. alginolyticus
, and isocitrate lyase AceA, the key enzyme involved in glyoxylate shunt, was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the late stage.

IMPORTANCE

Biofilms pose serious public problems, not only protecting the cells in it from environmental hazard but also affecting the composition and abundance of bacteria, algae, fungi, and protozoa. The important opportunistic pathogen
Vibrio alginolyticus
is extremely ubiquitously present in seawater, and it also exhibited a strong ability to form biofilm; thus, investigation on the biofilm formation of
V. alginolyticus
at molecular level is fundamental for the deeper exploration of the environmental concerns arose by biofilm. In this study, transcriptome analysis of biofilm cells (BFs) and planktonic cells (PTs) from
V. alginolyticus
was performed and AceA was screened to play an important role in biofilm formation. AceA was shown to maintain biofilms accompanied by downregulation of flagellation but promoted dispersal of BFs at the disperse stage. This method was helpful to further understand the ability and mechanism of
V. alginolyticus
biofilm formation and provide clues for prevention of
V. alginolyticus
infection.
Complete genome sequence of a potentially probiotic cheese isolate
Lactiplantibacillus plantarum
LP140 from the Nordbiotic collection
Authors: Szczepankowska Agnieszka , Cukrowska Bożena , Aleksandrzak-Piekarczyk Tamara 
Published: October 2024

ABSTRACT

We report the complete genome sequence of
Lactiplantibacillus plantarum
LP140, a cheese isolate from the Nordbiotic collection, comprising 3,371,266 bp with 44.4% GC content. Our data provide insight into the potential of LP140 for use as a probiotic strain.
Ash deposits link Oceanic Anoxic Event 2 to High Arctic volcanism
Authors: Dummann Wolf , Wennrich Volker , Schröder-Adams Claudia J. , Leicher Niklas , Herrle Jens O. 
Published: October 2024

Abstract
Oceanic Anoxic Event 2 (OAE 2) was a major environmental perturbation that occurred ∼94 million years ago. It is associated with profound changes in global climate and carbon cycling, which are commonly attributed to large-scale carbon release from large igneous province (LIP) volcanism. However, the specific LIP(s) involved and the mechanisms of carbon release remain poorly understood, as indicated by discrepancies between carbon release rates suggested by numerical models and LIP degassing estimates. Our study refines the eruptive history of the High Arctic large igneous province (HALIP) by dating ashfall deposits in marine sediments from the Canadian High Arctic using an integrated stratigraphic approach. Our results show that silicic HALIP volcanism began tens of thousands of years before OAE 2, suggesting a strong causal link. Volcanic activity coincides with a marked shift in carbon isotope values, linked to the degassing of HALIP magmas and/or thermogenic gas release. We propose that the concurrent activity of two LIPs—the HALIP and the Kerguelen Plateau—could account for the high rates of carbon release inferred for OAE 2, providing a hypothesis for its pervasive environmental impact.
Supplemental Material: Origin of the Oligocene–Miocene Sailipu ultrapotassic volcanic rocks in southern Tibet: Melting of Asian mantle pyroxenites triggered by eastward tearing of the subducting Indian continental slab
Authors: Liu Lin , al. et 
Published: October 2024

<p>Table S1: The mineral assemblage, whole-rock major and trace element data for the Sailipu ultrapotassic rocks. Table S2: U-Pb age data of zircons from Sailipu ultrapotassic rocks. Table S3: Trace element data of zircons from Sailipu ultrapotassic rocks. Table S4: Hf isotopic data of zircons from the Sailipu ultrapotassic rocks. Table S5: Major element and trace element data of olivine from Sailipu ultrapotassic rocks. Table S6: Major element and trace element data of clinopyroxene from Sailipu ultrapotassic rocks. Table S7: Estimation of redox condition of the Sailipu ultrapotassic rocks based on olivine-liquid equilibrium. Table S8: Estimation of crystallization temperature of the Sailipu ultrapotassic rocks based on olivine-liquid equilibrium. Table S9: Estimation of crystallization temperature and pressure of the Sailipu ultrapotassic rocks based on clinopyroxene-liquid equilibrium. Table S10: Pressure-temperature estimates of the Sailipu ultrapotassic rocks. </p>
Fungal community composition varies spatially in a commercial potato field in response to soil properties and topographic features
Authors: Neupane Saraswoti , Goyer Claudia , Zebarth Bernie J. , Li Sheng , Mills Aaron , Whitney Sean 
Published: October 2024

The factors influencing the spatial distribution of fungal communities are commonly examined over large spatial scales but not at smaller scales. Given this, the extent to which soil properties and topographic features contribute to the diversity and distribution of fungal communities in an agricultural field needs to be further explored. We investigated the spatial distribution of soil fungal community composition from an ∼1100 m long transect with 83 sampling points in a commercial potato field with a rolling landform. The relative abundance of Ascomycota, Basidiomycota, and Mortierellomycota showed medium to strong spatial dependence with an autocorrelation range varying from ∼43 to 92 m, similar to the autocorrelation range of soil properties and topographic features. Most of the variability in fungal and saprotrophic community composition was explained by soil properties (15% and 11%, respectively) and spatial distance (16% and 15%, respectively) while topographic features contributed 8% and 5% of variability to total fungi and saprotrophic community composition, respectively. The fungal and saprotrophic community compositions were correlated with soil organic carbon, pH, and slope curvature, however, richness and Pielou’s evenness of the fungal communities and fungal biomass were not correlated with soil properties or topographic features. The results suggest that the spatial variation in fungal and saprotrophic community composition in response to soil properties and topographic features in this agricultural landscape was due to differences in assemblages of fungal amplicon sequence variants (ASVs) but not in differences in the number of fungal ASVs or fungal biomass measured using phospholipids fatty acids.
Charmless decays of the spin-2 partner of X(3872)
Authors: Cai Zu-Xin , Jia Zhao-Sai , Li Gang , Liu Shi-Dong , Xie Ju-Jun 
Published: October 2024

AbstractThe Belle collaboration recently reported a pro-mising candidate for the spin-2 $$D^*\bar{D}^*$$

D
∗

D

¯

∗

partner of the X(3872), called the $$X_2$$

X
2

for short, having a mass of $$(4014.3 \pm 4.0 \pm 1.5)~\textrm{MeV}$$

(
4014.3
±
4.0
±
1.5
)

MeV

and a width of $$(4 \pm 11 \pm 6)~\textrm{MeV} $$

(
4
±
11
±
6
)

MeV

. In present work, we assume the $$X_2$$

X
2

as a pure molecule of the $$D^*\bar{D}^*$$

D
∗

D

¯

∗

under four cases, i.e., pure neutral components ($$\theta = 0$$

θ
=
0

), isospin singlet ($$\theta = \pi /4$$

θ
=
π
/
4

), neutral components dominant ($$\theta = \pi /6$$

θ
=
π
/
6

), and purely charged components ($$\theta = \pi /2$$

θ
=
π
/
2

), where $$\theta $$
θ
is a phase angle describing the proportion of neutral and charged constituents. Using an effective Lagrangian approach, we calculated the partial widths of $$X_2\rightarrow VV$$

X
2

→
V
V

and $$X_2 \rightarrow PP$$

X
2

→
P
P

(V and P stand for light vector and pseudoscalar mesons, respectively). The predicted decay widths of $$X_2 \rightarrow VV$$

X
2

→
V
V

can reach a few hundreds of $$\textrm{keV}$$
keV
, while the decay widths of $$X_2 \rightarrow PP$$

X
2

→
P
P

are about several tens of $$\textrm{keV}$$
keV
. In addition, the effects from the proportion of neutral and charged constituent on the decay widths of $$X_2\rightarrow VV$$

X
2

→
V
V

and PP are also investigated. We hope that the present calculations will be checked experimentally in the future.
The Role of Confirmatory Testing in Carpal Tunnel Syndrome: Electrodiagnostic Study, Ultrasound and CTS-6
Authors: GABRIEL Daniel C. , DEMETRI Leah , ZHANG Dafang 
Published: October 2024

Carpal tunnel syndrome (CTS) is the most common upper extremity compressive neuropathy. The reference standard for the diagnosis of CTS remains an area of controversy. The diagnosis can be established clinically, but options for confirmatory testing include electrodiagnostic studies, ultrasound and diagnostic aids such as the CTS-6 score. This review article summarises the current evidence for each confirmatory testing modality, contrasts their advantages and disadvantages and discusses future directions for investigation. Level of Evidence: Level V (Diagnostic)
Assessment of Fracture Line Angle in Mallet Fractures
Authors: ATEŞ Erdem , GÜMÜŞOĞLU Ender , ARIKAN Anıl , ESKANDARİ Metin Manouchehr 
Published: October 2024

Background: Surgery is often offered to patients with mallet fractures that have a large, displaced fragment and/or joint subluxation. However, the surgical approach remains a subject of debate, and surgery is frequently associated with unsatisfactory outcomes. We felt that the angle formed by the fracture line and the long axis of the distal phalanx on a lateral view radiograph (fracture line angle [FLA]) could be useful in determining the appropriate treatment strategy. The aim of this study was to assess the FLA and its distribution in mallet fractures. Methods: Three researchers measured the mallet FLA and the percentage of articular surface (PAS) involved in the lateral radiographs of 103 patients with a mallet fracture. Results: There was a strong correlation between the mallet FLA and the percentage of joint surface involvement between the three researchers. The mean FLA was 42.59° (±11.54) and it ranged from −1 to +1 standard deviation in 73 individuals (70.87%). The FLA varied over a wide range, while clustering near the average value. The average PAS involvement was 46.5% (±8.7%). There was no correlation between FLA and PAS involvement (p > 0.05). Conclusions: It is possible to quantify the mallet FLA accurately and consistently. It varies widely, regardless of the PAS involvement. When choosing the type of treatment and making prognostic predictions, the mallet FLA may be a helpful guide. Level of Evidence: Level IV (Diagnostic)
The Transverse Sigmoid Notch Morphology Unravelled
Authors: KRAMER Simon B. , RAAD Frederike , HAUSER Alexander , SCHIPPER Inger B. , SCHEP Niels W. L. 
Published: October 2024

Background: Several studies have described pathology in relation to transverse sigmoid notch morphology, using the Tolat transverse sigmoid notch classification. It is believed that the entire shape of a sigmoid notch can be described using Tolat sigmoid types. We hypothesised that the determination of the sigmoid notch shape (SNS) depends on the level of the transverse CT plane on the axial axis of the distal radius. The aim of this study was to determine and compare the transverse SNS on different axial CT levels in the same wrist. Methods: The transverse SNS of 53 participants were independently qualitatively classified by two researchers in accordance with the four morphologies described by Tolat et al. The SNS was determined at two levels on the axial axis of the distal radius; at the level of the most prominent part of Lister tubercle, determined on the sagittal plane and at the level of the ‘smallest distance between the ulnar head and sigmoid notch’ (SDUS). Results: Forty-seven percent of the wrists demonstrated different SNS types according to Tolat classification, depending on the axial level of the CT scan. Interobserver agreement on the transverse sigmoid shape was 87% at Lister tubercle and 85% at SDUS, which can both be interpreted as ‘excellent’. Conclusions: Despite an excellent interobserver agreement, 47% of the study population had different transverse sigmoid notch types within the same wrist. We, therefore, conclude that Tolat transverse sigmoid classification may not be useful for the description of potential pathology in relation to the sigmoid notch morphology.
Formal Security Analysis of the OpenID FAPI 2.0 Family of Protocols: Accompanying a Standardization Process
Authors: Hosseyni Pedram , Küsters Ralf , Würtele Tim 
Published: October 2024

FAPI 2.0 is a suite of Web protocols developed by the OpenID Foundation’s FAPI Working Group (FAPI WG) for third-party data sharing and digital identity in high-risk environments. Even though the specifications are not completely finished, several important entities have started to adopt the FAPI 2.0 protocols, including Norway’s national HelseID, Australia’s Consumer Data Standards, as well as private companies like Authlete and Australia-based connectID; the predecessor FAPI 1.0 is in widespread use with millions of users.
The FAPI WG asked us to accompany the standardization of the FAPI 2.0 protocols with a formal security analysis to proactively identify vulnerabilities before widespread deployment and to provide formal security guarantees for the standards. In this paper, we report on our analysis and findings.
Our analysis is based on a detailed model of the Web infrastructure, the so-called Web Infrastructure Model (WIM), which we extend to be able to carry out our analysis of the FAPI 2.0 protocols including important extensions like FAPI-CIBA. Based on the (extended) WIM and formalizations of the security goals and attacker model laid out in the FAPI 2.0 specifications, we provide a formal model of the protocols and carry out a formal security analysis, revealing several attacks. We have worked with the FAPI WG to fix the protocols, resulting in several amendments to the specifications. With these changes in place, we have adjusted our protocol model and formally proved that the security properties hold true under the strong attacker model defined by the FAPI WG.