bluuebunny/crossref_metadata_2025 huggingface dataset:
In Tandem With Artificial Intelligence: A working Framework for Coding in ATLAS.ti™
Authors: Williamson Charmaine , van Rooyen Annelien , Dry Rika
Published: February 2025

As a leading qualitative researcher, Norman Denzin advocated for a bigger tent to expand and deepen qualitative inquiry. The “tent” metaphor has therefore been used by scholars to advocate for considerations of diverse options around philosophies of inquiry. With the advent of Artificial Intelligence (AI), researchers face additional options around research decisions, philosophically, practically and ethically. Researchers table numerous research questions around AI, given its rapid uptake. These include re-visiting the established notions of human-centered coding, as well as exploring the potential of AI coding, within these notions. There is therefore room to expand “the tent” to delineate 1) the specific use of AI within qualitative data analysis, specifically AI coding, which is now an established function within bespoke qualitative data analysis software (QDAS). Additionally, with AI providing a stream of independent coding, 2) researchers may well deliberate the need for multiple, second or independent coders. This paper responds to this two-fold aim of the study using action research that involved researchers doing coding and using independent coding, in tandem with AI. The contribution of the paper is an outline of these action steps, reflectively culminating in a practical framework. This may be used by researchers, both curious and confident, in seeking novel ways to broaden the scope of their coding practices.
Eye on context: Individual differences reveal the mechanisms of statistical learning
Authors: Zinchenko Artyom , Conci Markus , Müller Hermann J , Geyer Thomas
Published: February 2025

If a searched-for target object is consistently encountered within repeating spatial distractor arrangements, target detection becomes more efficient relative to nonrepeated, that is, random arrangements (contextual cueing [CC] effect). However, target location changes within otherwise unchanged distractor arrays substantially weaken the cueing effect. Previous studies reported substantial variations in individual participants’ abilities to learn and relearn invariant contexts. Therefore, the current study examined how individual differences in attentional control and focus, as indexed by the well-established Stroop and Navon tasks, respectively, relate to CC in a learning phase/relocation phase design. During the visual search, we recorded behavioural reaction times (RTs) and fixation locations, the latter permitting us to decompose search RTs into search- and motor-related substages. We could thus evaluate the processes responsible for CC and the lack thereof after target relocation while also testing whether search and motor components of CC are different for individuals depending on their Stroop/Navon scores. Repeated contexts yielded faster RTs (and reduced fixation numbers), though there was a substantial decrease in cueing from learning to adaptation, consistent with previous studies. Critically, contextual learning, but not relearning, varied across individuals: participants with high-Stroop interference displayed overall larger CC during early target search, while a more local Navon task bias was associated with increased CC during later processes of target response decisions. Our results demonstrate that analysing individual differences can help validate the processes responsible for CC in search tasks, particularly distinguishing between early search and later response-related mechanisms.
Long-term functional outcomes among patients surviving aneurysmal subarachnoid hemorrhage: The KOSCO study
Authors: Lee Ho Seok , Sohn Min Kyun , Lee Jongmin , Kim Deog Young , Shin Yong-Il , Oh Gyung-Jae , Lee Yang-Soo , Joo Min Cheol , Lee So Young , Song Min-Keun , Han Junhee , Ahn Jeonghoon , Lee Young-Hoon , Kim Dae Hyun , Kim Young-Taek , Kim Yun-Hee , Chang Won Hyuk
Published: February 2025

Background and objectives:

Aneurysmal subarachnoid hemorrhage (aSAH) remains a significant global health concern, and therefore, understanding their functional outcomes is essential. The aim of this study was to investigate the 1-year functional outcomes of patients with aSAH.

Methods:

We retrospectively analyzed data of patients with aSAH from the Korean Stroke Cohort for Functioning and Rehabilitation study, up to 1 year post-onset. The cohort data were collected twice. The first data was collected from August 2012 through May 2015, and the second data was collected from January to December in 2020, from nine different hospitals. Assessments were performed from 7 days to 1 year. Disability, measured by modified Rankin Scale (mRS), was analyzed in terms of good outcome (mRS 0 or 1) and mortality. In addition, functional level was further assessed using Functional Independence Measure (FIM) in aSAH survivors at 1 year post-onset. A subgroup analysis was conducted, with participants further classified into two groups: one with mild-to-moderate disability (mRS 0–3) and another with severe disability (mRS 4 or 5), as reported 7 days after onset. Multiple imputation method was used to handle missing data. In addition, mixed-effects model was used to analyze the trajectory of FIM.

Results:

A total of 517 patients with aSAH were included. Of these, 246 (47.6%) showed mild-to-moderate disability and 271 (52.4%) showed severe disability at 7 days. At 1 year after onset, the mortality rate was 6.0% and the good outcome was reported in 76.2% of patients. In aSAH survivors at 1 year, FIM showed a significant improvement over time, with a significant difference demonstrated between the subgroups. Age, initial clinical severity, and cognitive function at 7 days were also identified as significant covariates.

Conclusions:

The majority of patients reporting mild-to-moderate disability at 7 days exhibited good functional outcome, and even among those with severe disability, there was a favorable outcome with continuous improvement in their functional levels. Therefore, proper assessments and effective management should be employed to achieve favorable functional outcomes among aSAH survivors.
New era, new GOALs: cardiovascular screening and lipid management in cystic fibrosis
Authors: Despotes Katherine A. , Ceppe Agathe S. , Goralski Jennifer L. , Donaldson Scott H.
Published: February 2025

Background:

Cardiovascular disease (CVD) risks are increasing in people with cystic fibrosis (pwCF). While cholesterol levels were historically low in pwCF, higher levels after initiating highly effective modulator therapy (HEMT) have been reported. Mechanisms are unclear and there is little guidance on screening.

Objectives:

To evaluate serum lipid changes at multiple timepoints after ivacaftor initiation, and to assess current screening practices for CVD risk factors among CF providers.

Design:

This was a post-hoc correlative analysis of prospectively collected clinical data and serum samples from the GOAL cohort study. Cross-sectional survey methodology was also employed.

Methods:

We evaluated serum lipids (total cholesterol (TC), low-density lipoprotein (LDL), and high-density lipoprotein (HDL)) at baseline, 3- and 18 months after ivacaftor initiation using samples from the GOAL study biorepository. We also surveyed CF providers across the United States on their CVD risk screening practices.

Results:

Fifty GOAL participants’ samples were analyzed. Using the repeated measures model, TC significantly varied by visit ( p = 0.004), driven by a significant increase from baseline at 3 months (mean difference 9.4 mg/dL). This difference diminished by 18 months. BMI was a significant covariate for TC. No significant differences by visit were detected in LDL or HDL. Seventy-five respondents participated in the survey (response rate 5.6%; 41 adult providers, 18 pediatric providers, and 10 providers caring for both) with 67% reporting no lipid screening policy existed in their center. In the past year, 29% of adult providers prescribed lipid-lowering therapy, 54% started anti-hypertensive medications, and 48% initiated ischemic cardiac evaluations for pwCF.

Conclusion:

TC significantly increased within 3 months of initiating ivacaftor, but subsequently diminished toward baseline by 18 months. Lipid screening practices among CF providers were variable and providers are increasingly being confronted with managing CVD risk factors. Partnering with primary care providers is likely to become increasingly important in CF care models.
Impact of carotid artery tortuosity on mechanical thrombectomy outcomes: A systematic review
Authors: Bilgin Cem , Gupta Rishabh , Orscelik Atakan , Hassankhani Amir , Senol Yigit Can , Kobeissi Hassan , Ghozy Sherief , Kadirvel Ramanathan , Brinjikji Waleed , Kallmes David F.
Published: February 2025

Background

Carotid artery tortuosity (CAT) may complicate mechanical thrombectomy (MT), potentially causing delays or preventing recanalization. However, the relationship between CAT and MT outcomes remains largely unexplored. This systematic review aims to evaluate the existing evidence regarding the impact of CAT on MT outcomes.

Methods

Following PRISMA guidelines, a systematic literature search was conducted using MEDLINE, EMBASE, Web of Science, Cochrane, and Scopus databases. Studies providing data for MT outcomes based on CAT status were included. Outcomes of interest included successful recanalization, first-pass efficacy (FPE), procedure time, functional independence, and procedure-related complications.

Results

Our search identified nine studies with 2737 patients. Three studies employed DSA to assess tortuosity, whereas the remaining six studies preferred CTA. In seven studies, CAT was associated with prolonged procedure times. In five studies, successful recanalization rates were significantly lower in CAT patients as compared to patients with non-tortuous arteries. Two studies showed that CAT could alter FPE or successful recanalization rates of first-line MT techniques. No study found statistically significant relationships between CAT and functional independence. Three studies examined the association between CAT and safety outcomes, and only one study found increased intracranial hemorrhage rates in patients with CAT. All nine studies employed different CAT criteria.

Conclusions

Despite the vast MT literature, the number of studies reporting CAT status remains low. CAT may affect procedure time and technical outcomes of MT. Therefore, employing a uniform CAT definition and reporting CAT more frequently can provide insights into management of patients with acute large vessel occlusions.
“I gave in and I’m not proud . . . ”: When responsible consumers transgress their personal norms
Authors: Rogeon Fabien , Montmasson-Peyre Stéphanie , Martins-Felix Sophie
Published: February 2025

Being a responsible consumer represents a daily challenge and there are many obstacles to implementing responsible behaviors. Past research has underlined the gap between pro-environmental attitudes and effective behaviors, highlighting obstacles to the adoption of responsible behaviors. However, it has hitherto not looked at the transgressions of consumers who adopt responsible behaviors in their daily lives. To address this gap, our research adopts a qualitative approach, based on semi-directive interviews conducted using the critical incident technique. Our analysis revealed several reasons why responsible consumers transgress their personal norms, and how these “consumer green transgressions” are managed by the responsible consumers. We also established a typology of “consumer green transgressions” based on a double categorization: anticipated versus impulsive transgressions and repetitive versus exceptional transgressions. Finally, we highlighted two “cause(s) → transgression → consequence(s)” trajectories. The results of this research offer several theoretical contributions and managerial implications, including discussing the literature on “green gap.”
Comparing the Efficacy of XP-endo Finisher with Irrigation Activation Methods on Sealer Penetration: An in Vitro Confocal Laser Scanning Microscopy Study
Authors: Akgun Ceyda , Gunes Betul
Published: February 2025

Aim:

The irrigation method is effective on the dentinal tubule penetration (DTP) of endodontic pastes, which is important for treatment outcome. The purpose of this study was to compare the effect of different irrigation techniques on the DTP of bioceramic endodontic paste with CLSM.

Materials and Methods:

A total of 52 mandibular premolar root canals were shaped with the ProTaper Next files and were divided randomly into four experimental groups ( n = 13) according to the final irrigation method with 17% EDTA and 5.25% NaOCl as follows: Group 1: Conventional needle irrigation (CNI), Group 2: sonic activation (SA), Group 3: passive ultrasonic activation (PUA), Group 4: XP-endo Finisher (XPF). After final irrigation, root canals were obturated with a bioceramic sealer labeled with the fluorescent dye. The roots were sectioned horizontally at three different levels, and 1 ± 0.1 mm thick sections were obtained to examine under CLSM. The penetration area (PA), maximum tubule penetration (MTP), and the percentage of penetration (PP) values were statistically evaluated with the two-way repeated measurements ANOVA test. The Tukey (HSD) test was carried out for intergroup comparisons ( p < .01). The relationship between the MTP, PP, and PA at each root level was evaluated using Pearson’s correlation test.

Results:

In the middle sections, the penetration area of the sealer was higher in the SA group (7.120 ± 1.470) compared to the other groups ( p < .01). Penetration area was higher in the XPF group (11.830 ± 1.370) in the coronal section compared to CNI (7.034 ± 0.926) ( p < .01). No significant difference was observed between the MTP and PP values of the experimental groups ( p > .01). DTP of sealer was statistically similar for each irrigation method in the apical section. The coronal regions showed higher DTP values compared with the apical regions. There was a linear relationship between the PA and MTP values at all root levels of experimental groups ( p < .05). The linear relationship between the PA and PP was not significant in the XP group ( p > .05).

Conclusion:

The penetration area of SA was larger than others in the middle section, and XPF was superior to CNI in the coronal section. DTP of the sealer in the apical regions was lower than in the coronal regions.
Cannabis Marketing Strategies in the United States: A Descriptive Analysis of Four Prominent Companies
Authors: LoParco Cassidy R. , Cui Yuxian , McCready Darcey M. , Rossheim Matthew E. , Chen-Sankey Julia , Howlader Afrah , Fergnani Anna , Mumin Deqa , Burris Scott , Berg Carla J.
Published: February 2025

Background:

Given the substantial expansion of the US cannabis market and the impact of cannabis advertising exposure on use, cannabis marketing surveillance is needed to inform regulations and protect consumers.

Methods:

Using 2020–2021 Vivvix advertising data from 4 US cannabis companies (Cresco, Mindy’s, MedMen, and Uncle Ike’s), we examined (1) general advertising characteristics (eg, number of unique ads and ad occurrences, ad expenditures, market, and media channel); and (2) ad content (ie, headlines and imagery) and placement (ie, source themes, eg, specific websites and magazines), overall and by company.

Results:

There were 399 unique ads and 1171 occurrences, totaling $488,617 in expenditures. Cresco and Uncle Ike’s accounted for most unique ads (~45% each); Cresco represented the majority of ad occurrences (52.4%) and expenditures (63.4%). Most ads were disseminated via online displays (occurrences = 69.2%; expenditures = 45.8%). The primary source for ad dissemination was news/weather (occurrences = 36.3%; expenditures = 40.2%). Ad headlines most frequently emphasized product type (occurrences = 40.1%; expenditures = 37.0%). Visual strategies to attract attention included gifs (occurrences = 63.6%; expenditures = 71.1%). Companies differed in their marketing strategies (ie, volume, markets, channels, and content).

Conclusions:

Findings underscore the need to restrict cannabis marketing, for example, restricting ad content and marketing channels. This may reduce exposure to cannabis marketing, which is associated with cannabis perceptions and use.
Preoperative prediction of flexible ureteroscopy outcome in the treatment of renal calculi
Authors: Abozaid Mohammed , Elsherif Eid , Elserafy Fatma , Abobakr Islam , Selim Mohamed
Published: February 2025

Background

Retrograde intrarenal surgery (RIRS) is increasingly used for management of renal calculi. Many predictive scores have been devised to predict stone-free rate (SFR) after RIRS including Ito’s nomogram. The aim of this study is to evaluate preoperative parameters that affect SFR after RIRS to help with patient counselling.

Methods

Patients with renal stones up to 30 mm in greatest diameter were recruited. They were offered RIRS via disposable flexible ureteroscopy and Holmium laser fragmentation. Ito’s score was calculated for each patient preoperatively to estimate post-operative SFR. Also, other factors as stone Hounsfield units (HU), pre-stenting, and access sheath use were recorded.

Results

A total of 80 patients met the inclusion criteria. Median stone volume was smaller in cases that were stone free (532.4 vs 748.0 mm3, p = 0.076). Patients with residuals had higher rates of multiple (61.5% vs 16.7%, p < 0.001) and lower pole (61.5%vs 37.0%, p = 0.039) calculi. Hydronephrosis, operator experience, HU, access sheath use, pre-stenting, and total Ito score were not significantly different between stone-free patients and patients with residuals. Multivariate logistic regression showed that presence of multiple renal stones (B = 0.158, p = 0.002) is the only significant predictor of SFR.

Conclusion

Larger stones, stones in the lower pole, and especially multiple renal stones have higher rates of residual stones after RIRS. This should be clarified to patients during preoperative decision-making and discussion about RIRS and its alternatives’ pros and cons has to take place prior to surgery.

Trial registration: Trial registered at clinicaltrial.gov, under number NCT05857501 on May 10th, 2023. https://clinicaltrials.gov/study/NCT05857501.
Opioid sparing anesthesia in patients with liver cirrhosis undergoing liver resection: a controlled randomized double-blind study
Authors: Ibrahim Eman Sayed , Metwally Ahmed A. , Abdullatif Mohamed , Eid Essam A. , Mousa Mahmoud G. , Sultan Amany A.
Published: February 2025

Objective

Opioid metabolism and pharmacodynamics may be affected in hepatic patients. Ketamine and dexmedetomidine are conventional anesthetics used in our daily practice. The opioid-sparing effects of this combination have not been evaluated in patients with liver cirrhosis undergoing liver resection. We aimed to investigate the potential peri-operative opioid-sparing effects of intra-operative dexmedetomidine and ketamine infusions in patients with Child A liver cirrhosis undergoing liver resection.

Methods

This study was a randomized controlled double-blind trial. 92 adult patients of both sex with Child class (A) liver cirrhosis aged 18 to 65 years entering and completing the study. We excluded patients with renal or cardiac dysfunction or contraindications from study medications.46 patients in the opioid-sparing group (OS) receiving ketamine and dexmedetomidine infusions and 46 patients in the opioid-based (OB) group as controls. The main outcome measures: were intra-operative fentanyl requirements, postoperative fentanyl requirements, visual analogue pain scores, postoperative nausea, vomiting, ileus, desaturation, intra-operative hemodynamic events, and ICU stay were recorded.

Results

The total intra-operative fentanyl consumption was significantly lower in the OS group compared with the OB group, 183.2 ± 35.61 µg and 313.5 ± 75.06 µg, respectively, P < 0.001. The postoperative 1st 48 h fentanyl consumption was significantly lower in the OS group compared with the OB group, 354.5 ± 112.62 µg and 779.1 ± 294.97 ± µg, respectively, P < 0.001. Visual analogue scores were significantly better in the OS group at the early 2-hour assessment point postoperatively. The postoperative adverse events were significantly more frequent in the opioid-based group. ICU stay was significantly shorter in the OS group.

Conclusions

Administering dexmedetomidine and ketamine infusions intra-operatively to patients with Child A liver cirrhosis undergoing liver resection resulted in notable opioid-sparing effects, with reductions of approximately 40% intra-operatively and 55% postoperatively. The opioid-sparing group exhibited improved postoperative outcomes, including reduced pain, decreased incidence of opioid-related side effects and shorter ICU stays.
Adaptations to the welsh national exercise referral scheme during the COVID-19 pandemic: a qualitative study exploring the experiences of service users and providers and supplementary out-of-pocket cost analysis
Authors: Newby Katie , Howlett Neil , Wagner Adam P. , Lloyd Nigel , Freethy Imogen , Bontoft Charis , Fakoya Olujoke , Jackson Shelley , Jackson Carla , Wills Wendy , McKibben Mary-Ann , Petherick Annie , Brown Katherine E.
Published: February 2025

Background

Despite the proliferation of exercise referral schemes in the UK, evidence on their efficacy is equivocal. The Welsh National Exercise Referral Scheme (NERS) is heavily used but inequalities in uptake have been reported. As a result of the COVID-19 pandemic, NERS was initially suspended and then transitioned from standard face-to-face delivery to alternative remote methods, including virtual delivery. The aim of this study was to explore the barriers and facilitators to uptake and engagement of NERS when delivered in face-to-face and virtual formats, and to examine the cost to service users of engaging with the scheme in these different ways.

Methods

This was a qualitative study with supplementary cost analysis. Maximum variation sampling was used to recruit participants. Interviews with service users (n = 21) and one person who declined the service, and three focus groups with service providers (n = 19), were conducted. Framework analysis was used to analyse the qualitative data. Quantitative data obtained through the interviews on service users’ out-of-pocket costs of attending face-to-face or virtual classes were summarised using descriptive statistics.

Results

Five themes were identified from the qualitative analysis which summarised barriers and facilitators to uptake and engagement as perceived and experienced by the different stakeholders. Themes included: opaqueness and uncertainty around referral; Exercise Referral Professionals allaying concerns and providing reassurance at scheme entry; the mixed appeal and accessibility of virtual delivery; factors that support ongoing engagement; and personal and financial circumstances restricting uptake and engagement.

Conclusions

This study indicates that offering a virtual version of NERS could make the scheme more accessible to those who are typically underserved, provided strategies to address digital inclusion are addressed. Findings provide wider evidence to inform adaptations that could be made to ensure that other exercise referral schemes can optimise virtual delivery.
Confronting needlestick and sharp injuries in healthcare: a decade of struggle and progress in a university teaching hospital
Authors: Wong Shuk-Ching , Yuen Lithia Lai-Ha , Lam Germaine Kit-Ming , Kwok Monica Oi-Tung , Siu Crystal Yuen-Ki , Li Bella Hong-Yan , Chen Jonathan Hon-Kwan , So Simon Yung-Chun , Chiu Kelvin Hei-Yeung , Cheng Vincent Chi-Chung
Published: February 2025

Background

Needlestick and sharp injuries (NSIs) among healthcare workers (HCWs) are a significant concern in infection prevention. This study analyzes the incidence and characteristics of NSIs at Queen Mary Hospital and assesses the effectiveness of targeted training programs for interns.

Methods

A retrospective analysis was conducted on NSI reports from 2014 to 2023, focusing on episodes involving medical, nursing, allied health, and other staff. Personal coaching training programs for newly recruited interns were implemented in 2019 to enhance safety practices. NSI episodes were analyzed in relation to patient days and full-time equivalents (FTE).

Results

During the study period, there was a mean of 464,118 patient days per year, with an average of 5,928 HCWs per year. A total of 1,076 NSI episodes were reported, resulting in a mean of 2.31 episodes per 10,000 patient days and 1.82 episodes per 100 FTE. Medical staff accounted for 502 episodes (47%), while nursing staff had 339 episodes (32%). The mean NSI episodes among medical staff were significantly higher than nursing staff per year, measured per 10,000 patient days (1.08 ± 0.21 vs. 0.73 ± 0.16, p = 0.001) and per 100 FTE (8.46 ± 1.95 vs. 1.62 ± 0.40, p < 0.001). Of the 1,076 episodes, 430 (40%) occurred in HCWs with less than 1 year of experience, with 278 (65%) attributed to interns, contributing to 26% of the overall NSI burden. Most incidents among interns occurred in wards (95%, 264/278), with 95% (252/264) involving hollow needles. Notably, 54% (149/278) involved safety-equipped devices, yet 94% (140/149) of these were not activated properly. Following targeted training, NSI rates among interns significantly decreased from 0.82 to 0.46 per 10,000 patient days (R2 = 0.977, p = 0.001) and from 6.84 to 3.40 per 100 FTE (R2 = 0.874, p = 0.020) from 2019 to 2023.

Conclusions

The study highlights the ongoing issue of NSIs among HCWs, especially inexperienced interns. While training programs have shown promise in reducing NSI rates, the high incidence of safety devices not being effectively utilized underscores the need for continuous education and hands-on training to enhance safety practices and prevent NSIs in healthcare settings.
A comparative analysis of sequence composition in different lots of a phage display peptide library during amplification
Authors: Sinkjaer Anders Wilgaard , Sloth Ane Beth , Andersen Amanda Oester , Jensen Malte , Bakhshinejad Babak , Kjaer Andreas
Published: February 2025

Background

To develop efficient selection strategies and improve the discovery of promising ligands, it is highly desirable to analyze the sequence composition of naïve phage display libraries and monitor the evolution of their peptide content during successive rounds of amplification. In the current study, we performed a comparative analysis of the compositional features in different lots of the same naïve phage display library and monitored alterations in their peptide compositions during three rounds of amplification.

Methods

We conducted three rounds of duplicate serial amplification of two different lots of the Ph.D.™-12 phage display library. DNA from the samples was subjected to Next-Generation Sequencing (NGS) using an Illumina platform. The NGS datasets underwent a variety of bioinformatic analyses using Python and MATLAB scripts.

Results

We observed substantial heterogeneity in the sequence composition of the two lots indicated by differences in the enhanced percentage of wildtype clones, reduced diversity (number of unique sequences), and increased enrichment factors (EFs) during amplification as well as by observing no common sequence between lots and decreased number of common sequences between the naïve library and the consecutive rounds of amplification for each lot. We also found potential propagation-related target-unrelated peptides (TUPs) with the highest EFs in the two lots, which were displayed by the fastest-propagating phage clones. Furthermore, motif analysis of the most enriched subpopulation of amplified libraries led to the identification of some motifs hypothesized to contribute to the increased amplification rates of the respective phage clones.

Conclusion

Our results highlight tremendous heterogeneity in the peptide composition of different lots of the same type of naïve phage display library, and the divergent evolution of their compositional features during amplification rounds at the amino acid, peptide, and motif levels. Our findings can be instrumental for phage display researchers by bringing fundamental insights into the vast extent of non-uniformity between phage display libraries and by providing a clear picture of how these discrepancies can lead to different evolutionary fates for the peptide composition of phage pools, which can have profound impacts on the outcome of phage display selections through biopanning.
High, but variable prevalence of Sarcocystis cruzi infections in farm-raised American bison (Bison bison) beef destined for human consumption
Authors: de Araujo Larissa S. , Gupta Aditya , Papadopoulos Marianne Dias , Naguib Doaa , Battle Jacquin , Kwok Oliver , Khan Asis , Rosenthal Benjamin , Dubey Jitender P.
Published: February 2025

Background

Bison (Bison bison) and cattle (Bos taurus) are closely related (can interbreed) and they also share many parasites. Cattle are commonly infected with one or more of the eight named Sarcocystis species: Sarcocystis hirsuta, S. cruzi, S. hominis, S. bovifelis, S. heydorni, S. bovini, S. sigmoideus and S. rommeli. Among these, the full life-cycle is known only for S. cruzi. Sarcocystis cruzi (transmitted via canids) is recognized as the most pathogenic Sarcocystis species, causing abortion, low milk yield and poor body growth. It has been experimentally cross-transmitted from cattle to bison and vice versa.

Methods

We tested 200 bison tongues from three commercial sources (farms) (Nebraska #141; South Dakota #36; New Jersey and Pennsylvania #23). Frozen tongues were purchased and examined for Sarcocystis infection using light microscopy, histology and quantitative PCR (qPCR) targeting 18S ribosomal DNA (18S rRNA) of S. cruzi. Lesions associated with degenerating sarcocysts were studied. The intensity of Sarcocystis infection in histological sections was quantitated.

Results

Sarcocystis cruzi-like infections were detected in 129 of 141 (91.5%) tongues from Nebraska, 36 of 36 (100%) tongues from South Dakota and two of 23 (8.6%) tongues from New Jersey and Pennsylvania. Sarcocysts were detected in histological sections stained with hematoxylin and eosin in 167 of 200 samples. Light microscopy examination revealed that the sarcocysts had thin walls (< 1 µm thick) and appeared to be S. cruzi. However, in two samples, sarcocysts had thicker walls measuring up to 2.3 µm wide and 154 µm long and the sarcocyst wall was not striated; these two samples could not be characterized further. In three tongues, degenerating sarcocysts were recognized; two of these were associated with thick-walled sarcocysts. Molecularly, S. cruzi from bison was identical to that in cattle.

Conclusions

In the present study of bison tongues, S. cruzi was the only species identified in bison using both molecular and morphological methods. An unidentified species of Sarcocystis found in two bison samples needs further study.

Graphical abstract
β-Hydroxybutyrate-induced mitochondrial DNA (mtDNA) release mediated innate inflammatory response in bovine mammary epithelial cells by inhibiting autophagy
Authors: Huo Yihui , Shen Taiyu , Feng Tianyin , Li Moli , Zhao Wanli , Loor Juan J. , Aernouts Ben , Psifidi Androniki , Xu Chuang
Published: February 2025

Background

In perinatal dairy cows, ketosis is a prevalent metabolic disorder that lowers milk output and performance. Mitochondrial dysfunction and chronic inflammation in mammary tissue are linked to elevated blood ketone levels, particularly β-hydroxybutyrate (BHB). Recent research has linked cytosolic mitochondrial DNA (mtDNA) with chronic aseptic inflammation by activating the cGAS-STING pathway during metabolic disorders, while autophagy activation effectively reverses this process. However, whether it is involved in mammary gland damage during ketosis is poorly understood. Therefore, this study aimed to explore the underlying mechanisms of mtDNA-induced inflammation under BHB stress and evaluate the potential therapeutic strategy of autophagy activation in mitigating this damage.

Results

Our study found an increased cytoplasmic mtDNA abundance in mammary gland tissues of dairy cows with ketosis and bovine mammary epithelial cell line (MAC-T) subjected to BHB stress. Further investigations revealed the activation of the cGAS-STING pathway and inflammatory response, indicated by elevated levels of cGAS and STING, along with increased phosphorylation levels of TBK1, P65, and IκB, and higher transcript levels of pro-inflammatory factors (IL-1B, IL-6, and TNF-α) in both in vivo and in vitro experiments. Notably, STING inhibition via si-STING transfection reversed BHB-induced inflammation. Additionally, autophagy activation appeared to protect against BHB stress by facilitating the removal of cytoplasmic mtDNA and preventing cGAS-STING pathway-mediated inflammation.

Conclusions

The findings illustrate that elevated BHB levels lead to the release of cytoplasmic mtDNA, which in turn activates the cGAS-STING pathway and triggers an inflammatory response in the mammary glands during hyperketonemia. Conversely, autophagy activation has been shown to alleviate this process by promoting cytoplasmic mtDNA degradation.

Graphical Abstract
Impact of climate and human-induced fire on the Dongyuan Lake, Southern Taiwan during the last 1850 cal years BP
Authors: Rahman Abdur , Wang Liang-Chi , Yu Neng-Ti , Yen Jiun-Yee
Published: February 2025

This study investigates the relationship among the wildfires, climate, and humans and their combined impact on the Dongyuan Lake in southern Taiwan using a sediment core that covered the last 1850 cal years BP. Charcoal accumulation rate (CHAR) peaks, low total organic carbon (TOC), total nitrogen (TN), TOC/TN ratios, and carbon isotopic composition (δ13Corg), combined with low sedimentation rate (SR) and silt dominance suggested a loss of organic carbon, no or low runoff and soil instability due to wildfires during 1850–1700, 1600–1450, and 1350–1100 cal years BP. This led to silt dominance, further indicating drier climatic conditions. Two intermittent wet phases during 1700–1600 and 1450–1350 cal years BP, indicated by high TOC, TN, TOC/TN ratios, and δ13Corg, suggested peatland formation. After 1100 cal years BP, increased runoff, and organic matter accumulation indicated peatification, suggesting wetter conditions characterized by higher TOC, TN, TOC/TN ratios, δ13Corg, and SR. Wetter periods continued, but the appearance of diatoms indicated shallow water levels during 750–500 cal years BP and from 350 cal years BP to the present. CHAR peaks suggest wildfire activity, and combined with archaeological evidence, this implies human-induced burning during these periods. The variation in pH and nutrient dynamics (indicated by PCA analysis of diatoms) were closely linked to wildfire intensity and frequency. Infrequent wildfires (750–500 cal years BP) caused lake acidification, while frequent fires (350 cal years BP to present) raised pH. In the past 150 years, human activities, mainly deforestation and acid rain, have contributed to lake acidification.
The impact of a 1 mm interimplant distance on the interproximal crestal bone height: a case report with a 10-year follow-up and literature review
Authors: Morales Schwarz David , Szmukler-Moncler Serge , Morales Melendez Hilde , Beuer Florian
Published: February 2025

Background

Between adjacent dental implants, an interimplant distance (IID) of at least 3 mm has been recommended to avoid resorbing the interproximal crestal bone. The effect of a 2 mm IID on crestal bone loss has been investigated but the literature is scarce when it comes to an IID of 1 mm. There is a need to document such clinical situations when they occur and elucidate if such a narrow IID is deleterious or not to the interproximal crest. The present case deals with an IID of 1 mm in the premolar area where, for the first time, the fate of an interimplant crest is reported after a 10-year follow-up.

Case presentation

A 57-year-old patient attended with 2 hopeless maxillary premolars. The mesio-distal space available for implant rehabilitation was too narrow to receive standard diameter implants and keep an inter-implant distance (IID) of 3 mm as recommended by accepted guidelines. A protocol of immediate implant placement and provisionalization involving 2 implants of Ø 3.5 mm was implemented; placement in the extraction sockets resulted in an IID of 1 mm. After 3 months of healing the final prosthesis was delivered; the patient has been followed for 10 years now. Surprisingly, the findings showed that the interimplant crest was maintained 1.40 mm coronal to the shoulder of the neck of the implants. Bone completely filled the space between the prosthetic concave abutments and the interproximal papilla was closing the embrasure. The literature reports only 2 experimental studies involving a 1 mm IID; both showed that this did not lead to the resorption of the interproximal bone.

Conclusions

Unexpectedly, the present case with an IID of 1 mm did not lead to the resorption of the interproximal bone after 10 years. It is speculated that the reason for that is due to the implants displaying an internal conical connection, the platform-switching feature, concave abutments and subcrestal placement. The fate of the interproximal crest of implants placed with an IID of 1 mm lacks scientific evidence. More studies are warranted to elucidate this question in order to propose the best implant treatment in cases displaying a limited mesio-distal space.
Association between chronic obstructive pulmonary disease and osteoporosis: Mendelian randomization combined with bibliometric analysis
Authors: Yang Fangjun , Wang Huaming , Liu Miaomiao , Pei Shengtai , Qiu Xiaoming
Published: February 2025

Background

Previous observational studies have reported an association between chronic obstructive pulmonary disease (COPD) and osteoporosis (OP). The aim of this study is to investigate the causal relationship between COPD and OP by two-sample Mendelian randomization (MR) analysis. The current status of cross-sectional research between COPD and OP in the past decade was explored through bibliometrics.

Methods

Single nucleotide polymorphisms (SNPs) that have been found to be strongly associated with COPD were used as instrumental variables (IVs) in MR Analysis. The primary outcome of the study was BMD measurement at five specific anatomical sites, namely the whole body, femoral neck, lumbar spine, forearm, and heel. These BMD measurements were derived primarily from a genome-wide association study (GWAS) and summary statistics from the International Genetic Factors Consortium for Osteoporosis (GEFOS). The main analysis method was inverse variance weighting (IVW). Multiple sensitivity analyses were performed to assess the robustness and reliability of the current MR Results. Further confirmatory MR Analysis between COPD and OP was applied. In bibliometrics. Publications were extracted from the Web of Science core collection publications related to osteoporosis and sarcopenia published between January 2014 and October 2024; Bibliometrics and visualization were performed by Microsoft Office Excel, Citespace, and R (Bibliometrix).

Results

The MR Findings suggest that there is no causal relationship between COPD and BMD at five specific anatomical sites. The results of the primary IVW MR Analysis were generally supported by our sensitivity MR Analysis. We performed MR Analysis for the validation of COPD and OP (IVW OR: 1.019; 95%CI: 0.898–1.564; p = 0.768) also did not support a causal relationship between COPD and BMD. A total of 471 articles written by 1119 organizations from 42 countries/regions by 3331 authors and published in 238 journals were identified in the bibliometric analysis. China is the leading country in terms of the number of publications. China Medical University contributed the most publications. The International Journal of Chronic Obstructive Pulmonary Disease has the highest publication in this field.

Conclusions

In conclusion, This MR Study found no causal relationship between COPD and OP, suggesting that the observed associations may be due to common genetic effects or environmental confounders. The global research trends in this field in the past decade were summarized through bibliometric analysis, and care became the focus of future research on the relationship between copd and OP.
Contrastive learning in building vision-language models for subsurface geoscience
Authors: Aseev Anatoly , Huang Jiayuan , Mishra Priya
Published: February 2025

This paper presents the potential of contrastive language-image pretraining (CLIP) in subsurface geoscience, both as a standalone tool for multimodal semantic search and within the broader context of vision-language model training. This paper focuses on the role of CLIP in developing subsurface-specific vision-language models and presents a novel workflow for the stochastic generation of meaningful subsurface image-text data sets, adaptable for any vision-language training. Using this workflow, a synthetic geologic and seismic image-caption data set are constructed to conduct training experiments with CLIP. A comparison of training strategies for subsurface classification and semantic search reveals that CLIP models using domain-specific pretrained encoders deliver superior accuracy compared with traditional CLIP pretraining with off-the-shelf encoders. Additionally, we introduce GeoGen, a machine learning tool designed to generate realistic geologic and seismic models from textual descriptions in which domain-trained CLIP models play a pivotal role. Evaluation of GeoGen's performance emphasizes the importance of selecting an appropriate CLIP training strategy to enhance vision-language fusion and improve model quality.
Advancing geologic document digitalization and information retrieval with generative AI
Authors: Hou Song , Dong Tianhao , Sancheti Ojasvi , Liu Hao
Published: February 2025

This paper demonstrates how generative artificial intelligence (AI) enhances geoscientific document processing by improving text analysis, table extraction, and figure classification. Traditional workflows struggle with domain-specific terminology, poor-quality inputs, and rare formats. To address these challenges, we employ domain fine-tuned bidirectional encoder representations from transformers (BERT) models to enhance text processing. Additionally, we utilize multimodal large language models for precise table recognition and context-aware image classification. Finally, a domain-optimized retrieval system, GeoRAG, improves the relevance and accuracy of information retrieval. These AI-driven advancements streamline digitalization, enhance data extraction, and enable efficient handling of complex geoscientific documents. While challenges such as hallucinations, interpretability, and output consistency remain, this study highlights the transformative potential of generative AI for geoscience workflows and decision-making processes.
Capabilities of text-to-text large language models in seismic velocity estimation of CO2- or H2-saturated rocks
Authors: Masaya Shogo
Published: February 2025

Since the release of ChatGPT in 2022, generative artificial intelligence powered by large language models (LLMs) has gained significant traction, demonstrating its potential across various fields. This study explores the capability of pretrained text-to-text LLMs in rock physics modeling, focusing specifically on estimating seismic velocities in CO2- or H2-saturated rocks. Such estimations are essential for subsurface gas storage, a crucial component in advancing the energy transition and achieving decarbonization goals. These gas injections alter rock elastic properties, such as seismic velocities and density, necessitating accurate monitoring. While existing methods rely on theories, empirical relations, and machine learning, these methods face challenges like data scarcity and model uncertainty. We evaluate four popular language models — GPT-4o, GPT-4o mini, GPT-4 turbo, and Claude 3.5 Sonnet — in blind tests using experimental benchmark data to assess their ability to optimize model selection and parameter determination in rock physics.
Simulating seismic wavefields using generative artificial intelligence
Authors: Nakata Rie , Nakata Nori , Ren Pu , Bi Zhengfa , Lacour Maxime , Erichson Benjamin , Mahoney Michael W.
Published: February 2025

Simulating realistic seismic wavefields is crucial for a range of seismic tasks, including acquisition designing, imaging, and inversion. Conventional numerical seismic wave simulators are computationally expensive for large 3D models, and discrepancies between simulated and observed waveforms arise from wave equation selection and input physical parameters such as the subsurface elastic models and the source parameters. To address these challenges, we adopt a data-driven artificial intelligence approach and propose a conditional generative modeling (CGM) framework for seismic wave simulation. The novel CGM framework learns complex 3D wave physics and subsurface heterogeneities from the observed data without relying on explicit physics constraints. As a result, trained CGM-based models act as stochastic wave-propagation operators encoded with a local subsurface model and a local moment tensor solution defined by training data sets. Given these models, we can simulate multicomponent seismic data for arbitrary acquisition settings within the area of the observation, using source and receiver geometries and source parameters as input conditional variables. In this study, we develop four models within the CGM framework — CGM-GM-1D/3D, CGM-Wave, and CGM-FAS — and demonstrate their performance using two seismic data sets: a small low-density data set of natural earthquake waveforms from the San Francisco Bay Area, a region with high seismic risks, and a large high-density data set from induced seismicity records of the Geysers geothermal field. The CGM framework reproduces the waveforms, the spectra, and the kinematic features of the real observations, demonstrating the ability to generate waveforms for arbitrary source locations, receiver locations, and source parameters. We address key challenges, including data density, acquisition geometry, scaling, and generation variability, and we outline future directions for advancing the CGM framework in seismic applications and beyond.
Reviews
Authors: Aitken Julie
Published: February 2025

Mineral Systems, Earth Evolution, and Global Metallogeny, by David Ian Groves and M. Santosh, 2023