bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial composition and diversity in intraradicular biofilm formed in situ: New concepts based on next‐generation sequencing
Authors: Matoso Felipe Barros , Montagner Francisco , Grecca Fabiana Soares , Rampelotto Pabulo Henrique , Kopper Patrícia Maria Poli 
Published: March 2024

AbstractThis study aimed to characterize the taxonomic composition of intraradicular multispecies biofilms (IMBs) formed in situ in a model to reproduce clinical conditions. Twelve palatal roots of maxillary molars had its canals prepared. Two roots were randomly selected to sterility control. Ten intraoral prosthetic appliances with lateral slots were fabricated. The roots were positioned in the slots with the canal access open to the oral cavity. Eight volunteers wore the appliance for 21 days, and two wore it at two different time points. One root from each appliance was removed and stored at −20°C until DNA extraction and sequencing (n = 10). Biofilm was analyzed using next‐generation sequencing and bioinformatics. The V4 hyper‐variable region of the 16SrRNA gene was amplified and sequenced. For data analyses, the mothur pipeline was used for 16SrRNA processing, and subsequent analyses of the sequence dataset were performed in R using the MicrobiomeAnalyst R package. The taxonomy‐based analysis of bacterial communities identified 562 operational taxonomic units (OTUs), which belonged to 93 genera, 44 families, and 8 phyla. Bacterial colonization was different for each biofilm, and samples did not have the same group of bacteria. Alpha and beta diversity analysis revealed some general patterns of sample clustering. A core microbiome of prevalent OTUs and genera was identified. IMBs were heterogeneous when analyzed individually, but some diversity patterns were found after sample clustering. The experimental model seemed to reproduce the actual biofilm composition in endodontic infections, which suggests that it may be used to evaluate disinfection protocols.
Symmetries and Representation
Authors: Hall Geoffrey , Murgueitio Ramírez Sebastián 
Published: March 2024

AbstractIt is often said in physics that if two models of a theory are related by a symmetry, then the two models provide (or could provide) two different representations of the very same situation, alike the case of two maps of different color for the very same city. It is also said that the situations represented by two models of a theory are indiscernible in some ways when the models in question are related by a symmetry of the theory, just like the situation in the interior of the cabin of a train when the train is at rest in the station is empirically indiscernible from the situation in the interior when the train is moving uniformly (in classical mechanics, these two situations are represented by two models related by a boost). In recent years, philosophers of physics have focused a lot of attention in developing various principles that aim to elucidate these and similar remarks on symmetries, models, physical equivalence, and representation that are widespread in physics practice. The goal of the current article is to provide a critical review of these principles, and suggest a new framework for thinking about these kinds of questions. One important upshot of the paper is that questions of indiscernibility, and questions of the representational capacity of models, must be distinguished from one another.
Diffusion Generative Model-Based Learning for Smart Layer-Wise Monitoring of Additive Manufacturing
Authors: Yangue Emmanuel , Fullington Durant , Smith Owen , Tian Wenmeng , Liu Chenang 
Published: March 2024

Abstract
Despite the rapid adoption of deep learning models in additive manufacturing (AM), significant quality assurance challenges continue to persist. This is further emphasized by the limited availability of sample objects for monitoring AM-fabricated builds. Thus, this study advances an emerging diffusion generative model, i.e., the denoising diffusion implicit model (DDIM), for layer-wise image augmentation and monitoring in AM. The generative model can be used to generate potential layer-wise variations, which can be further studied to understand their causation and prevent their occurrence. The proposed models integrate two proposed kernel-based distance metrics into the DDIM framework for effective layer-wise AM image augmentation. These newly proposed metrics include a modified version of the kernel inception distance (m-KID) as well as an integration of m-KID and the inception score (IS) termed KID-IS. These novel integrations demonstrate great potential for maintaining both similarity and consistency in AM layer-wise image augmentation, while simultaneously exploring possible unobserved process variations. In the case study, six different cases based on both metal-based and polymer-based fused filament fabrication (FFF) are examined. The results indicate that both the proposed DDIM/m-KID and DDIM/KID-IS models outperform the four benchmark methods, including the popular denoising diffusion probabilistic models (DDPMs), and three other generative adversarial networks (GANs). Overall, DDIM/KID-IS emerges as the best-performing model with an average KID score of 0.840, m-KID score of 0.1185, peak signal-to-noise ratio (PSNR) of 18.150, and structural similarity index measure (SSIM) of 0.173, which demonstrated strong capabilities in generating potential AM process variations in terms of layer-wise images.
Comparison of Two-Wheel and Four-Wheel Steering Using Event-Triggered Predictive Motion Control and Scale Vehicles
Authors: Zhou Zhaodong , Rother Christopher , Chen Jun 
Published: March 2024

Abstract
This study compares the trajectory tracking performance of two- and four-wheel steering systems, especially under normal driving conditions. Specifically, the lateral motion is controlled by an event-triggered model predictive control (MPC), which activates either when consecutive control steps surpass the predictive horizon or when tracking error exceeds a predetermined lateral offset. Using a modified 1/10th scale Tamiya TT-02 RC car as a test platform, the tracking performance of both two- and four-wheel systems are evaluated. Results from the experiments highlight the better tracking performance of the four-wheel steering system over the traditional two-wheel systems and demonstrate the benefit of using event-triggered MPC for lateral motion control even under normal driving conditions, contrary to common belief that four-wheel steering systems are beneficial only in tight steering maneuvers.
A novel glycoside hydrolase 43-like enzyme from
Clostridium boliviensis
is an endo-xylanase and a candidate for xylooligosaccharide production from different xylan substrates
Authors: Salas-Veizaga Daniel Martin , Rocabado-Villegas Leonardo Roberto , Linares-Pastén Javier A. , Gudmundsdottir Elisabet Eik , Hreggvidsson Gudmundur Oli , Álvarez-Aliaga María Teresa , Adlercreutz Patrick , Nordberg Karlsson Eva 
Published: March 2024

ABSTRACT

An uncharacterized gene encoding a glycoside hydrolase family 43-like enzyme from
Clostridium boliviensis
strain E-1 was identified from genomic sequence data, and the encoded enzyme,
CbE1
Xyn43-l, was produced in
Escherichia coli. CbE1
Xyn43-l (52.9 kDa) is a two-domain endo-β-xylanase consisting of a C-terminal CBM6 and a GH43-like catalytic domain. The positions of the catalytic dyad conserved in GH43, the catalytic base (Asp74), and proton donor (Glu240) were identified in alignments including GH43-enzymes of known 3D-structure from different subfamilies.
CbE1
Xyn43-l is active at pH 7.0–9.0, with optimum temperature at 65°C, and a more than 7 days’ half-life in irreversible deactivation studies at this temperature. The enzyme hydrolyzed birchwood xylan, quinoa stalks glucuronoarabinoxylan, and wheat arabinoxylan with xylotriose and xylotetraose as major hydrolysis products.
CbE1
Xyn43-l also released xylobiose from
p
NPX
2
with low turnover (
k
cat
of 0.044 s
−1
) but was inactive on
p
NPX, showing that a degree of polymerization of three (DP3) was the smallest hydrolyzable substrate. Divalent ions affected the specific activity on xylan substrates, which dependent on the ion could be increased or decreased. In conclusion,
CbE1
Xyn43-l from
C. boliviensis
strain E-1 is the first characterized member of a large group of homologous hypothetical proteins annotated as GH43-like and is a thermostable endo-xylanase, producing xylooligosaccharides of high DP (xylotriose and xylotetraose) producer.

IMPORTANCE

The genome of
Clostridium boliviensis
strain E-1 encodes a number of hypothetical enzymes, annotated as glycoside hydrolase-like but not classified in the Carbohydrate Active Enzyme Database (CAZy). A novel thermostable GH43-like enzyme is here characterized as an endo-β-xylanase of interest in the production of prebiotic xylooligosaccharides (XOs) from different xylan sources.
CbE1
Xyn43-l is a two-domain enzyme composed of a catalytic GH43-l domain and a CBM6 domain, producing xylotriose as main XO product. The enzyme has homologs in many related
Clostridium
strains which may indicate a similar function and be a previously unknown type of endo-xylanase in this evolutionary lineage of microorganisms.
Capsid-dependent lentiviral restrictions
Authors: Twentyman Joy , Emerman Michael , Ohainle Molly 
Published: March 2024

ABSTRACT

Host antiviral proteins inhibit primate lentiviruses and other retroviruses by targeting many features of the viral life cycle. The lentiviral capsid protein and the assembled viral core are known to be inhibited through multiple, directly acting antiviral proteins. Several phenotypes, including those known as
Lv1
through
Lv5
, have been described as cell type-specific blocks to infection against some but not all primate lentiviruses. Here we review important features of known capsid-targeting blocks to infection together with several blocks to infection for which the genes responsible for the inhibition still remain to be identified. We outline the features of these blocks as well as how current methodologies are now well suited to find these antiviral genes and solve these long-standing mysteries in the HIV and retrovirology fields.
Clinical characteristics of postoperative necrotizing enterocolitis in patients with congenital jejunoileal atresia and its risk factors
Authors: Xiong Xiaofeng , Lu Wei , Xing Fuzhong , Cai Yuan , Yang Jixin , Yuan Yuhang , Feng Jiexiong , Chen Xuyong 
Published: March 2024

ObjectiveTo review postoperative necrotizing enterocolitis (NEC) in patients with jejunoileal atresia (JIA) and to explore the potential risk factors related to the concurrence of NEC.MethodsPatients diagnosed with JIA who received surgical treatment from January 2016 to June 2021 were enrolled. Demographics, viral infection of the fetus, transfusion within 48 hours before NEC, sepsis before JIA repair, pathological and anatomical classification of JIA, combined malformation, occurrence time of NEC after the operation, treatment, and prognosis of patients were analyzed. Patients were divided into NEC group and non-NEC group, and all patients were followed up for 3–6 months to observe for complications.ResultsA total of 180 patients with JIA were included, of whom 12 were diagnosed with NEC after surgery and 1 patient with NEC died during follow-up. The average age, birth weight, gestational age, proportion of premature infants, proportion of preoperative infections, and pathological classification of JIA did not significantly differ between the two groups. The probability of patients with proximal jejunal atresia (PJA) in the NEC group (58.3%) was higher than that in the non-NEC group (22.6%) (p=0.011), and patients with PJA had longer parenteral nutrition time than patients without PJA (26.64±9.21 days vs 15.11±6.58 days,p<0.001).ConclusionPJA was more likely to be associated with concurrent NEC after surgery, which is a highly NEC-related risk factor inherent in JIA.
Clinical Features and Classification of Proximal Carpal Fracture Dislocation Through the Radiocarpal Joint
Authors: XIONG Ge , ZHENG Wei , ZHU Jin 
Published: March 2024

Background: The most common types of wrist dislocation are trans-scaphoid lunate dislocation (TLD) and trans-scaphoid perilunate dislocation, in which the lunate and proximal scaphoid are dislocated through the midcarpal joint. There is another rare type of dislocation in which the proximal carpi are dislocated through the radiocarpal joint. The purpose of this study is to examine the clinical features of this type of dislocation. Methods: Six cases of the proximal carpal fracture dislocation via the radiocarpal joint were retrospectively reviewed. All patients underwent open reduction and internal fixation with the ligament reconstruction. A Mayo wrist score was assigned to each patient based on the assessment of pain, functional status, range of motion and grip strength at the last follow-up. Clinical subjective evaluation of function and pain was assessed using the patient-rated wrist evaluation (PRWE) method. Results: All patients were male and injured with a median age of 33.5 years. The median follow-up period was 10 months. There were three types of dislocations: Scaphoid fracture dislocation, TLD and scaphoid-lunate dislocation. All patients had satisfactory results with an average PRWE of 7.2 ± 4.7. The preoperative VAS was 6.7 ± 1.0 and the postoperative VAS was 0.7 ± 0.7 (p < 0.01). Postoperative grip strength accounted for 89.2% ± 9.8% of the contralateral side; the Mayo wrist score averaged 90.0 ± 6.5, with four patients obtaining excellent and two good results. Conclusions: Fracture dislocation of the proximal carpal bones through the radiocarpal joint is an independent type of wrist dislocation that tends to occur in young men with high-energy impact. The wrist is most often injured in a pronation hyperextension position. If treatment is timely and appropriate, the prognosis is quite good. Level of Evidence: Level IV (Therapeutic)
Carpal Tunnel Syndrome Caused by a Juxta-articular Myxoma: A Case Report
Authors: YANO Koichi , YONEDA Akira , OHTA Yoshio , KANESHIRO Yasunori 
Published: March 2024

Juxta-articular myxoma (JAM) is a rare soft tissue tumour predominantly composed of mucinous tissue and usually found around large joints. We report a 73-year-old woman with a 5-year history of a soft tissue mass in the thenar eminence of the right wrist who presented to our department. An initial diagnosis of a ganglion cyst was made using magnetic resonance imaging (MRI) and the jellied content of the mass by aspiration. Two years after presentation, surgical treatment with tumour resection and carpal tunnel release via the radial approach was performed because the symptoms of carpal tunnel syndrome worsened, and the tumour invaded the carpal tunnel. Histopathological examination revealed a JAM. At the 1-year follow-up, the symptoms of carpal tunnel syndrome had resolved, and no recurrence was confirmed by MRI. Level of Evidence: Level V (Therapeutic)
Application of Dual‐Layer Spectral‐Detector Computed Tomography Angiography in Identifying Symptomatic Carotid Atherosclerosis: A Prospective Observational Study
Authors: Zhang Jia , Li Sijia , Wu Lei , Wang Haoyuan , Wang Chuanying , Zhou Yinan , Sui Binbin , Zhao Xingquan 
Published: March 2024

Background
Dual‐layer spectral‐detector dual‐energy computed tomography angiography (DLCTA) can distinguish components of carotid plaques. Data on identifying symptomatic carotid plaques in patients using DLCTA are not available.

Methods and Results

In this prospective observational study, patients with carotid plaques were enrolled and received DLCTA. The attenuation for both polyenergetic image and virtual monoenergetic images (40, 70, 100, and 140 keV), as well as
Z
‐effective value, were recorded in the noncalcified regions of plaques. Logistic regression models were used to assess the association between attenuations of DLCTA and the presence of symptomatic carotid plaques. In total, 100 participants (mean±SD age, 64.37±8.31 years; 82.0% were men) were included, and 36% of the cases were identified with the symptomatic group. DLCTA parameters were different between 2 groups (symptomatic versus asymptomatic: computed tomography [CT] 40 keV, 152.63 [interquartile range (IQR), 70.22–259.78] versus 256.78 [IQR, 150.34–408.13]; CT 70 keV, 81.28 [IQR, 50.13–119.33] versus 108.87 [IQR, 77.01–165.88]; slope
40–140 keV
, 0.91 [IQR, 0.35–1.87] versus 1.92 [IQR, 0.96–3.00];
Z
‐effective value, 7.92 [IQR, 7.53–8.46] versus 8.41 [IQR, 7.94–8.92]), whereas no difference was found in conventional polyenergetic images. The risk of symptomatic plaque was lower in the highest tertiles of attenuations in CT 40 keV (adjusted odds ratio [OR], 0.243 [95% CI, 0.078–0.754]), CT 70 keV (adjusted OR, 0.313 [95% CI, 0.104–0.940]),
Z‐
effective values (adjusted OR, 0.138 [95% CI, 0.039–0.490]), and slope
40–140 keV
(adjusted OR, 0.157 [95% CI, 0.046–0.539]), with all
P
values and
P
trends <0.05. The areas under the curve for CT 40 keV, CT 70 keV, slope 40 to 140 keV, and
Z
‐effective values were 0.64, 0.61, 0.64, and 0.63, respectively.

Conclusions
Parameters of DLCTA might help assist in distinguishing symptomatic carotid plaques. Further studies with a larger sample size may address the overlap and improve the diagnostic accuracy.
Prognostic Implications of Left Atrial Strain in Bicuspid Aortic Valve With Chronic Aortic Regurgitation
Authors: Tan YuTing , Li YuMan , Deng WenHui , Zhang RuiZe , Zhao RuoHan , Abulipizi Abudukadier , Zhang Jing , Ji Xiang , Hou QuanFei , Liu Tianshu , Fang Lingyun , Zhang Li , Xie MingXing , Wang Jing 
Published: March 2024

Background
Left atrial reservoir strain (LARS) is a novel imaging biomarker of left ventricular diastolic dysfunction. This study aimed to examine the prognostic implications of LARS in patients with bicuspid aortic valve and significant (moderate‐severe to severe) aortic regurgitation.

Methods and Results

A total of 220 patients with bicuspid aortic valve and significant aortic regurgitation were prospectively enrolled in our study. LARS and left ventricular global longitudinal strain were derived from speckle‐tracking echocardiography. The end point was a composite of all‐cause mortality, heart failure hospitalization, and aortic valve repair or replacement. The threshold value of LARS <24% was used to identify impaired left atrial mechanics based on prior results. During a median follow‐up of 364 (interquartile range, 294–752) days, 46 patients (20.9%) reached the composite end points. On multivariable Cox analysis, impaired LARS (adjusted hazard ratio, 2.08 [95% CI, 1.05–4.11];
P
=0.036) was a statistically significant predictor of composite end points after adjustment for other statistically significant predictors. Finally, adding impaired LARS to other statistically significant predictors (New York Heart Association functional class and left ventricular global longitudinal strain) significantly improved the global χ
2
(from 32.19 to 36.56;
P
=0.037) and reclassification (continuous net reclassification index=0.55;
P
<0.001) of the prediction model.

Conclusions
In patients with bicuspid aortic valve and significant aortic regurgitation, the impairment of LARS is a strong independent prognostic predictor and confers incremental prognostic utility over clinical and other echocardiographic parameters. These findings suggest that LARS could be considered in risk stratification for such populations.
Functional MRI brain state occupancy in the presence of cerebral small vessel disease—a pre-registered replication analysis of the Hamburg City Health Study
Authors: Ingwersen Thies , Mayer Carola , Petersen Marvin , Frey Benedikt M. , Fiehler Jens , Hanning Uta , Kühn Simone , Gallinat Jürgen , Twerenbold Raphael , Gerloff Christian , Cheng Bastian , Thomalla Götz , Schlemm Eckhard 
Published: March 2024

Abstract
We aimed to replicate recent findings on the association between the extent of cerebral small vessel disease (cSVD), functional brain network dedifferentiation, and cognitive impairment. We analyzed demographic, imaging, and behavioral data from the prospective population-based Hamburg City Health Study. Using a fully prespecified analysis pipeline, we estimated discrete brain states from structural and resting-state functional magnetic resonance imaging (MRI). In a multiverse analysis, we varied brain parcellations and functional MRI confound regression strategies. The severity of cSVD was operationalized as the volume of white matter hyperintensities of presumed vascular origin. Processing speed and executive dysfunction were quantified using the Trail Making Test (TMT). We hypothesized a) that a greater volume of supratentorial white matter hyperintensities would be associated with less time spent in functional MRI-derived brain states of high fractional occupancy; and b) that less time spent in these high-occupancy brain states associated with a longer time to completion in part B of the TMT. High-occupancy brain states were characterized by activation or suppression of the default mode network. Every 5.1-fold increase in WMH volume was associated with a 0.94-fold reduction in the odds of occupying DMN-related brain states (P = 5.01×10−8). Every 5% increase in time spent in high-occupancy brain states was associated with a 0.98-fold reduction in the TMT-B completion time (P = 0.0116). Findings were robust across most brain parcellations and confound regression strategies. In conclusion, we successfully replicated previous findings on the association between cSVD, functional brain occupancy, and cognition in an independent sample. The data provide further evidence for a functional network dedifferentiation hypothesis of cSVD-related cognitive impairment. Further research is required to elucidate the mechanisms underlying these associations.
Firm-Level Uncertainty and the Transmission of Monetary Policy
Authors: Lakdawala Aeimit , Moreland Timothy 
Published: March 2024

Abstract
We show that firms which face higher uncertainty adjust their investment less in response to monetary policy shocks. We find corroborating evidence of this differential effect from firm-level stock returns on FOMC announcement days. Our results are consistent with a real options (or “wait-and-see”) channel whereby higher uncertainty dampens the response to changes in business conditions. Consistent with this mechanism the dampening effect is stronger for firms that face higher reversibility costs of investment.
Weak Identification in Low-Dimensional Factor Models with One or Two Factors
Authors: Cox Gregory Fletcher 
Published: March 2024

Abstract
This paper describes how to reparameterize low-dimensional factor models with one or two factors to fit weak identification theory developed for generalized method of moments models. Some identification-robust tests, here called “plug-in” tests, require a reparameterization to distinguish weakly identified parameters from strongly identified parameters. The reparameterizations in this paper make plug-in tests available for subvector hypotheses in low-dimensional factor models with one or two factors. Simulations show that the plug-in tests are less conservative than identification-robust tests that use the original parameterization. An empirical application to a factor model of parental investments in children is included.
A new species of Rhacophorus (Anura: Rhacophoridae) from Guangxi Province, China
Authors: RAO DING-QI , WILKINSON JEFFERY A. , LIU HUI-NING 
Published: March 2024

A new species of Rhacophorus is described from Guangxi Province, China. The new species, Rhacophorus minimus, is the smallest of the known green species of Rhacophorus, with a SVL averaging only 28.1 mm for males and 37.0 mm for females. Other characters that separate it from other green Rhacophorus species include a smooth bright green dorsum, lacking tubercles and pattern; a white stripe from tip of snout along the upper lip and shoulder to insertion of hind limbs; reduced webbing, less than a third of the length of outer fingers; and disc of the 3rd finger smaller than the diameter of the tympanum.