bluuebunny/crossref_metadata_2025_split huggingface dataset:
State of the Practice Worldwide: Developing Approaches to Transition from Active Remediation to Monitored Natural Attenuation
Authors: Adamson David T. , Hort Hiroko , Wilson John T. , Newell Charles J. , McHugh Thomas E. 
Published: January 2025

AbstractA landmark National Research Council report from 2013 emphasized the need to transition to passive or less resource‐intensive management strategies like monitored natural attenuation (MNA) at sites where pump‐and‐treat and active remedies are providing diminishing returns. While this report is now more than a decade old, the process for implementing this type of transition assessment is still not well understood by practitioners. The objective of this study was to help address this gap by developing a software tool (TA2 Tool) that aids in gathering and analyzing data that are relevant for a site‐specific transition assessment. The implications of site complexities on achieving remedial objectives are a key component of transition assessment. This free web‐based tool has modules that perform quantitative assessment of concentration trends and project the remediation timeframe based on the current remedial approach. It has modules that predict how remediation timeframes are influenced by matrix diffusion to assess if additional remediation is warranted. Crucially, it includes modules that evaluate MNA as a transition technology, specifically by looking at plume stability, natural attenuation rates, and projections of plume concentrations at a downgradient point of compliance in the absence of further active treatment. This new tool complements existing resources on technology optimization and transitions, including ITRC guidance. The value of performing these types of assessments is highlighted through empirical data and case studies that show that it is not necessary to operate pump‐and‐treat systems in perpetuity and that many sites with these systems have either transitioned to other technologies or been closed.
Comparison of the Histological Structure of an Anterior as well as a Posterior Biopsy From the Human Palate: A Comparative Study
Authors: Bienz Stefan P. , Kuonen Jasmine , Hüsler Jürg , Gadzo Naida , Hitz Sonja , Jung Ronald E. , Thoma Daniel S. 
Published: January 2025

ABSTRACTAimTo compare the histological structure of biopsies from the anterior and posterior regions of the human palate in order to gain insights into potential differences of soft tissue harvesting sites.MethodsThis comparative study involved 20 participants, from each of whom four samples from the palatal mucosa were collected. The biopsies were histologically processed and subsequently analysed. The thickness of the epithelium, lamina propria, and the length of the rete pegs were measured using a microscope. In addition, parameters such as collagen fibres, elastic fibres, elastic connective tissue, loose connective tissue and the background were measured.ResultsThe mean epithelial thickness was 0.42 mm anteriorly and 0.37 mm posteriorly. The mean thickness of the lamina propria was 0.81 mm anteriorly and 0.85 mm posteriorly. Within the region of interest, collagen fibres were significantly less abundant anteriorly than posteriorly (p = 0.016). The loose connective tissue showed a significantly higher occurrence in the anterior compared with the posterior sampling site (p = 0.004).ConclusionThis trial indicates no differences in terms of the thickness of the lamina propria. There was a higher concentration of collagen fibres and a lower concentration of loose connective tissue in the posterior region of the palate.
Rarity and Sparseness in Plant Communities: Impact of Minor Species Removal on Beta Diversity and Canonical Ordination
Authors: Gillet François , Rouzet Adeline , Borcard Daniel , Legendre Pierre 
Published: January 2025

ABSTRACTQuestionAmong the “minor” species present in communities, we distinguish between true “rare” species, with infrequent occurrence (low occupancy) in a given regional data set, and “sparse” species, which may be present over most of the study area, but with low local abundance. Do rare and sparse species play a different role in the evaluation of beta diversity and in the constrained ordination of plant community data sets?MethodsBased on their positions in the abundance‐occupancy scatterplots of six contrasted vegetation data sets, we distinguished core, rural, urban, and satellite species. To disentangle the role of rarity and sparseness, we applied to each data set a progressive removal of either the least frequent or the least locally abundant species. We assessed impacts on beta diversity (q = 0, 1 and 2), and on model performance of RDA, without or after pretransformation of absolute cover values.ResultsMultiplicative beta diversity decreased with the number of removed rare species, with slightly higher values for q = 2, whereas it increased when removing sparse species, with much higher values for q = 0. With raw data or after binary or by‐site transformation, the fraction of variation explained by RDA increased only slightly when removing rare species, with a more sensible increase of the relative contribution of the first canonical axis. By contrast, progressive elimination of sparse species, which mimics a lower sampling effort within each community, negatively affected model performance. Generally, the removal of rare species clearly improved the performance of RDA after double transformation (chi‐square transformation), contrary to the removal of sparse species.ConclusionsThe frequently observed positive correlation between occupancy and abundance hides profound differences with critical impacts on vegetation analysis. Providing that meaningful transformations are applied, there is no need to remove rare species prior to RDA. Focusing only on abundant species during sampling is likely to limit the performance of ecological empirical models.
A best practice guide for conducting healthy food retail research: A resource for researchers and health promotion practitioners
Authors: Scapin Tailane , Boelsen‐Robinson Tara , Naughton Shaan , Ananthapavan Jaithri , Blake Miranda , Ferguson Megan , Gomez‐Donoso Clara , Gupta Adyya , Hobbs Victoria , McMahon Emma Joy , Romaniuk Helena , Sacks Gary , Thompson Julia , Alston Laura , Backholer Kathryn , Bennett Rebecca , Brimblecombe Julie , Chan Jasmine , Duus Katrine S. , Huse Oliver , Maganja Damian , Marshall Josephine , Orellana Liliana , Rosewarne Emalie , Schultz Sally , Sievert Katherine , Sherriff Simone , Tran Huong Ngoc Quynh , Vargas Carmen , Wu Jason H. Y. , Peeters Anna , Cameron Adrian J. 
Published: January 2025

SummaryRetail food environments play a pivotal role in influencing dietary behaviors, and therefore have huge potential as settings for promoting good nutrition and preventing obesity. Conducting research in retail settings can be challenging due to the varied motivations of the parties involved and the complex nature of retail environments. To improve the quality and consistency of research in this field, we have identified 16 thematic topics aimed at guiding researchers and public health practitioners on how to conduct healthy food retail research. A summary for each topic, encompassing existing methodologies, best practice examples, and knowledge gaps, was developed based on available literature and the collective experience and expertise of 32 multidisciplinary researchers from a high‐income perspective engaged in healthy food retail research in a diverse range of retail settings. A summary checklist describing key considerations at each stage of conducting healthy food retail research was also developed.
Plant‐based and sustainable diet: A systematic review of its impact on obesity
Authors: Mambrini Sara P. , Penzavecchia Claudia , Menichetti Francesca , Foppiani Andrea , Leone Alessandro , Pellizzari Marta , Sileo Federica , Battezzati Alberto , Bertoli Simona , De Amicis Ramona 
Published: January 2025

SummaryThe food system significantly affects the environment through land use, emissions from livestock, deforestation, and food waste. Diet sustainability considers the environmental effects of food production, distribution, and consumption. Animal products emit more greenhouse gases than plant‐based foods, prompting a shift towards plant‐focused diets for reduced emissions. Sustainable diets, like the EAT‐Lancet model, prioritize plant‐based foods, adjusting for regional eating habits. These diets aim to be both environmentally friendly and conducive to human health, addressing concerns like obesity and chronic diseases. Obesity is a major global health challenge, and its complex relationship with food production and consumption patterns calls for sustainable solutions to reduce pressure on ecosystems and promote healthier lifestyles. Tackling obesity requires holistic strategies that address not only individual health but also the broader environmental impacts of food systems. A systematic review examined the link between plant‐based diets and obesity focusing on studies assessing Body Mass Index (BMI) and body fat assessment. Despite limited research, evidence suggests that adherence to a plant‐based diet, particularly a healthy one, is associated with lower obesity rates. More longitudinal and intervention studies are necessary for a stronger consensus on the matter.
Trimethylamine N‐Oxide (TMAO) and TNF‐α Levels in Periodontal Disease Associated With Smoking
Authors: Bal Ipek , Balci Nur , Sorguc Cem , Toygar Hilal Uslu , Serdar Ceyhan C. , Kurgan Sivge , Serdar Muhittin A. 
Published: January 2025

ABSTRACTAimsTrimethylamine N‐oxide (TMAO) is a compound involved in the pathogenesis of various systemic inflammatory diseases, including cardiovascular conditions. The aim of this study was to determine differences in saliva and serum levels of TMAO between periodontitis and healthy patients according to smoking status.MethodsThe study included four systemically healthy groups: periodontally healthy non‐smokers (NS‐Control; n = 25), non‐smokers with Stage‐III‐Grade‐B periodontitis (NS‐Periodontitis; n = 25), periodontally healthy smokers (S‐Control; n = 25), and smokers with Stage‐III Grade‐C periodontitis (S‐Periodontitis; n = 25). Periodontal parameters were recorded. TMAO levels were determined in saliva and serum samples using liquid chromatography‐mass spectrometry (LC–MS/MS). TNF‐α levels were measured by the ELISA method.ResultsSalivary TNF‐α and TMAO levels were significantly elevated in the smoking periodontitis group compared to other groups (p < 0.001 and p = 0.003, respectively). Serum TMAO levels were also significantly higher in the smoking periodontitis group compared to non‐smoking controls and non‐smoking periodontitis. TMAO/SFR ratios were notably higher in the smoking periodontitis group compared to other groups, and a strong positive correlation was observed between salivary TMAO and TNF‐α levels (r = 0.892, p < 0.001).ConclusionThe data suggested that TMAO and TNF‐α are associated with inflammatory mechanisms of periodontitis in cases where periodontitis coexists with smoking.Trial RegistrationNCT06580431
Deep Learning for Staging Periodontitis Using Panoramic Radiographs
Authors: Li Xin , Chen Kejia , Zhao Dan , He Yongqi , Li Yajie , Li Zeliang , Guo Xiangyu , Zhang Chunmei , Li Wenbin , Wang Songlin 
Published: January 2025

ABSTRACTObjectivesUtilizing a deep learning approach is an emerging trend to improve the efficiency of periodontitis diagnosis and classification. This study aimed to use an object detection model to automatically annotate the anatomic structure and subsequently classify the stages of radiographic bone loss (RBL).Materials and MethodsIn all, 558 panoramic radiographs were cropped to 7359 pieces of individual teeth. The detection performance of the model was assessed using mean average precision (mAP), root mean squared error (RMSE). The classification performance was evaluated using accuracy, precision, recall, and F1 score. Additionally, receiver operating characteristic (ROC) curves and confusion matrices were presented, and the area under the ROC curve (AUC) was calculated.ResultsThe mAP was 0.88 when the difference between the ground truth and prediction was 10 pixels, and 0.99 when the difference was 25 pixels. For all images, the mean RMSE was 7.30 pixels. Overall, the accuracy, precision, recall, F1 score, and micro‐average AUC of the prediction were 0.72, 0.76, 0.64, 0.68, and 0.79, respectively.ConclusionsThe current model is reliable in assisting with the detection and staging of radiographic bone levels.
In-situ analysis of flow and morphology properties at the pore scale during CO2-Enhanced Oil Recovery
Authors: Wang Xin , Li Shaohua , Tong Baocai , Jiang Lanlan , Lv Pengfei , Ling Zheng , Song Yongchen 
Published: January 2025

Abstract
Enhanced oil recovery(CO2-EOR) is an essential technique to improve oil recovery while reducing greenhouse gas emissions. However, the pore-scale flow dynamics and morphological characteristics during the EOR process remain unclear. This study employs X-ray micro-tomography (micro-CT) to perform a displacement experiment through CO2 flooding. The pore characteristics, in situ wettability, morphological parameters, and interfacial area are analyzed. The spatial distribution of pores and throats is discovered to be even, with both radii distributions exhibiting narrow peaks. The coordination number is predominantly located between 5 and 10, increasing with pore size. As the displacement process proceeds, the percentage of contact angle distribution between 105° and 140° increases, indicating the ability of CO2 to remove the oil phase from the solid surface. As CO2 is injected, the oil-solid interfacial area decreases while the CO2-solid interfacial area increases, demonstrating the reduction in oil-wettability of the sample. The predominant form of residual gas at the end of displacement is residual film gas, characterized by positive Euler number values, indicating its existence as a disconnected phase. The isolated oil phase, characterized by a small volume and simple structure, dominates the remaining oil phase during CO2 injection. The surface area and volume of the oil phase exhibit a power-law relationship with similar coefficients and exponents at various pore volumes (PVs). Some larger oil phases deviate from the fitted curve, possibly due to dissolution.
Liposomal amphotericin B and complement activation-related pseudoallergy (CARPA)
Authors: Thompson George R. , Sani Gelina M. , Donnelley Monica A. , Figueroa Jaimie K. , Ciuffetelli Ryan , Trigg Kate , Arredondo Juan , Koff Alan , Nearing Marie , Loque Ikaika C. , Bays Derek J. , Dandekar Satya 
Published: January 2025

ABSTRACT

Infusion reactions (tachycardia, hypertension, fever, etc.) associated with liposomal amphotericin B are common. Animal models have found complement activation responsible, yet the pathophysiology has not been evaluated in human patients. We performed a prospective observational study and found complement activation-related pseudoallergy (CARPA) responsible in those with infusion reactions.
Control of
Clostridioides difficile
virulence and physiology by the flagellin homeostasis checkpoint FliC-FliW-CsrA in the absence of motility
Authors: Zhu Duolong , Wozniak Katherine J. , Midani Firas , Wang Shaohui , Sun Xingmin , Britton Robert A. 
Published: January 2025

ABSTRACT

Mutations affecting
Clostridioides difficile
flagellin (FliC) have been shown to be hypervirulent in animal models and display increased toxin production and alterations in central metabolism. The regulation of flagellin levels in bacteria is governed by a tripartite regulatory network involving
fliC
,
fliW
, and
csrA
, which creates a feedback system to regulate flagella production. Through genomic analysis of
C. difficile
clade 5 strains (non-motile), we identified they have jettisoned many of the genes required for flagellum biosynthesis yet retain the major flagellin gene
fliC
and regulatory gene
fliW
. We therefore investigated the roles of
fliC
,
fliW
, and
csrA
in the clade 5 ribotype 078 strain
C. difficile
1015, which lacks flagella and is non-motile. Analysis of mutations in
fliC
,
fliW
, and
csrA
(and all combinations) on
C. difficile
pathogenesis indicated that FliW plays a central role in
C. difficile
virulence as animals infected with strains carrying a deletion of
fliW
showed decreased survival and increased disease severity. These
in vivo
findings were supported by
in vitro
studies showing that mutations impacting the activity of FliW showed increased toxin production. We further identified that FliW can interact with the toxin-positive regulator TcdR, indicating that modulation of toxin production via FliW occurs by sequestering TcdR from activating toxin transcription. Furthermore, disruption of the
fliC-fliW-csrA
network results in significant changes in carbon source utilization and sporulation. This work highlights that key proteins involved in flagellar biosynthesis retain their regulatory roles in
C. difficile
pathogenesis and physiology independent of their functions in motility.

IMPORTANCE

Clostridioides difficile
is a leading cause of nosocomial antibiotic-associated diarrhea in developed countries with many known virulence factors. In several pathogens, motility and virulence are intimately linked by regulatory networks that allow coordination of these processes in pathogenesis and physiology. Regulation of
C. difficile
toxin production by FliC has been demonstrated
in vitro
and
in vivo
and has been proposed to link motility and virulence. Here, we show that clinically important, non-motile
C. difficile
strains have conserved FliC and regulatory partners FliW and CsrA, despite lacking the rest of the machinery to produce functional flagella. Our work highlights a novel role for flagellin outside of its role in motility and FliW in the pathogenesis and physiology of
C. difficile
.
Whole-genome sequence of
Salmonella enterica
subsp.
diarizonae
serovar 17: l,v:z: a new serovar isolated from a nose-horned viper in Republic of Serbia
Authors: Matović Kazimir , Galić Natasa , Vidanović Dejan , Šekler Milanko , Dmitrić Marko , Vasković Nikola , Debeljak Zoran , Tešović Bojana , Simović Aleksandar , Bošnjak Ivan , Krnjaić Dejan , Linde Jörg , Methner Ulrich 
Published: January 2025

ABSTRACT

We report the draft genome sequence of
Salmonella
enterica subsp.
diarizonae
serovar 17: l,v:z isolated from a nose-horned viper (
Vipera ammodytes
) in Republic of Serbia which might be considered a new serovar of
Salmonella
.
Diagnostic prediction model for screening of elevated low-density and non-high-density lipoproteins in young Thai adults between 20 and 40 years of age
Authors: Kiratipaisarl Wuttipat , Surawattanasakul Vithawat , Sirikul Wachiranun , Phinyo Phichayut 
Published: January 2025

BackgroundLow-density lipoprotein cholesterol (LDL-C) and non-high-density lipoprotein cholesterol (non-HDL-C) levels are paramount in atherosclerotic cardiovascular disease risk management. However, 94.4% of Thai young adult are unaware of their condition. A diagnostic prediction model may assist in screening and alleviating underdiagnosis.ObjectivesDevelopment and internal validation of diagnostic prediction models on elevated LDL-C (≥160 mg/dL) and non-HDL-C (≥160 mg/dL).MethodsRetrospective, single-centre, tertiary-care hospital annual health examination data from 29 March 2018 to 30 August 2023 was analysed. Two models with 11 predictors from anthropometry and bioimpedance are fitted with multivariable binary logistic regression predicting elevated LDL-C and non-HDL-C. Predictor selection used the backward stepwise elimination. Four performance metrics were quantified: discrimination using area under the receiver-operating characteristic curve (AuROC); calibration by calibration plot; utility by decision curve analysis and instability by performance instability plots. Internal validation was carried out using 500 repetitions of bootstrap-resampling.ResultsDataset included 2222 LDL-C and 5149 non-HDL-C investigations, 303 were classed as elevated LDL-C (13.6%) and 1013 as elevated non-HDL-C cases (19.7%). Two predictors, gender and metabolic age, were identified in the LDL-C model with AuROC 0.639 (95% CI 0.617 to 0.661), poor calibration, and utility in the 7%–25% probability range. Three predictors—gender, diastolic blood pressure and metabolic age—were identified in the non-HDL-C model with AuROC 0.722 (95% CI 0.705 to 0.738), good calibration and utility in 9%–55% probability range.Discussion and conclusionOverall results demonstrated acceptable discrimination for non-HDL-C model but inadequate performance of LDL-C model for clinical practice. An external validation study should be planned for non-HDL-C model.
Impact of introducing transnasal endoscopy on expanding diagnostic endoscopy services
Authors: Crosby Ben Thomas , Munglani Laura , Wright Karen , Charles Kay , Evans Wendy , Mathias Megan , Davies Stevie , Abdalla Badr , Turner Jeff , Crosby Tom , Trudgill Nigel , Haboubi Hasan 
Published: January 2025

IntroductionDemand for endoscopic services is outstripping capacity in the UK. Transnasal endoscopy (TNE) utilises a narrow calibre endoscope to pass through the nasal passages, thereby reducing retching and discomfort. It is better tolerated compared with standard transoral endoscopy (TOE) but is still rarely used as a diagnostic modality. There is still uncertainty about how well it performs against TOE in diagnostic ability, cost and efficiency.MethodsWe explored utilising TNE to deal with the growing demand for endoscopy. We compared findings to TOE procedures undertaken during the same time period. We evaluated cost differences, duration/time in the department for procedures as well as quality of procedures (both in terms of performance indicators as well as image quality using the validated POLPREP score).ResultsA total of 241 upper gastrointestinal endoscopy procedures were evaluated (100 TNE and 141 matched TOE) between December 2021 and February 2022. TNE outperformed TOE in obtaining >95% success rate in nationally approved key performance indicators (retroflexion and duodenal intubation, both p=0.026). It also was associated with better image quality in the oesophagus with a POLPREP A3 Score (excellent image quality) in 36/98 available images compared with 26/136 TOE (p=0.028) and was equivalent to TOE in the stomach and duodenum. TNE was identified as having a key role in facilitating complex cases, previously failed via the TOE route with a success rate in 11/12 (91.7%) of such cases. TNE also shows promise in correcting misdiagnoses of short-segment Barrett’s oesophagus (39%) compared with TOE (14.8%) (p=0.087).ConclusionTNE is an emerging endoscopic modality, which shows great promise in replacing TOE in most diagnostic circumstances. In a modern healthcare service, TNE is cheaper, better tolerated and outperforms TOE in multiple domains.
Pion Boer–Mulders function using a contact interaction
Authors: Cheng Dan-Dan , Cui Zhu-Fang , Ding Minghui , Roberts Craig D. , Schmidt Sebastian M. 
Published: January 2025

Abstract
A symmetry preserving treatment of a vector

$$\otimes $$

⊗

vector contact interaction (SCI) is used as the basis for calculations of the two pion transverse momentum dependent parton distribution functions (TMDs); namely, that for unpolarised valence degrees-of-freedom and the analogous Boer–Mulders (BM) function. Amongst other things, the analysis enables the following themes to be addressed: the quark current mass dependence of pion TMDs; the impact of the gauge link model on the positivity constraint that bounds the BM function relative to the unpolarised TMD; the equivalence of direct diagrammatic and light-front wave function TMD calculations; and the size of the BM shift. Interpreted astutely, these SCI results enable one to draw insightful pictures of pion TMDs.