bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation-based training for endoscopic mitral valve repair: the impact on basic surgical skills for placement of sutures at mitral valve annulus during 2-h training workshop
Authors: Checheili Sobbi Shokoufeh , Jung Yochun , Fillet Marvin , Bakhtiary Farhad , Maessen Jos G , Sardari Nia Peyman 
Published: January 2024

Abstract

OBJECTIVES
The aim of this study was to evaluate the impact of simulation-based training on surgical skills during 2-h learning labs during surgical annual meeting.

METHODS
During the 36th European Association of Cardiothoracic Surgery annual meeting a learning drylab for simulation-based training for endoscopic mitral valve repair was set up. For this purpose, a validated high-fidelity endoscopic mitral valve surgery simulator and a validated suturing map were used. The training lasted 2 h. Technical pre- and post-assessment were carried out based on time and accuracy to place a suture at the posterior mitral valve annulus. The suture had to be placed within 60 s. The suture was considered anatomically correct if it entered and exited the annulus at the designated place (on the posterior annulus) and accurate if placed within the right width (8–12 mm).

RESULTS
In total, 46 participants were included in this study, of whom 18 (38%) were experienced/staff surgeons, 23 (51%) fellows and 5 (11%) residents. Before the training, 48% of the participants failed to place any suture for pre-assessment. After completing the training, 100% of the participants succeeded in placing an anatomically correct suture. There was a significant improvement in the time taken [pre-assessment mean 45 (standard deviation: 25) s vs post-assessment mean 18 (standard deviation: 12) s, P &lt; 0.001] and the accuracy to place a suture in the mitral valve annulus after completing the training (pre-assessment 32.6% vs post-assessment 65.2%, P &lt; 0.001).

CONCLUSIONS
This study shows a significant improvement in endoscopic skills for mitral valve surgery after completing a 2-h training with a high-fidelity endoscopic mitral valve surgery simulator. This suggests that simulation trainings during scientific annual meetings are effective on surgical skills.
The cost of delay as risk measure in target-based multi-period portfolio selection models
Authors: Liu Jia , Chen Zhiping , Consigli Giorgio 
Published: January 2024

Abstract
Accepted by: Aris Syntetos
Increasingly, in recent years, the fund management industry has evolved towards so-called goal-based investing paradigms, under which investors are assumed to base their portfolio strategies on pre-specified targets to be attained in the future. A similar decision model is common in the wealth management and the life insurance industries where targets may be associated with long-term investment horizons and retirement planning problems. Based on this evidence, we propose in this article a novel risk measure explicitly focusing on the financial cost that may be associated with a delay in reaching those targets. We show that the definition of this risk measure is both rather natural and effective to capture investors’ risk preferences. A dynamic portfolio selection model is developed to assess the effectiveness of the risk measure from financial and risk control perspectives. The introduced risk measure has good properties and it is related to the Value-at-Risk with a given confidence level. Under sufficiently general statistical assumptions, we derive a closed form solution to a mean-risk formulation of the portfolio problem in which the cost of delay is taken as risk measure. Finally, a set of numerical tests validate the proposed portfolio selection model and show a set of comparative results with respect to a classical dynamic mean-variance model.
Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages
Authors: Dion Moïra B , Shah Shiraz A , Deng Ling , Thorsen Jonathan , Stokholm Jakob , Krogfelt Karen A , Schjørring Susanne , Horvath Philippe , Allard Antoine , Nielsen Dennis S , Petit Marie-Agnès , Moineau Sylvain 
Published: January 2024

Abstract
CRISPR–Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR–Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli’s CRISPR–Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR–Cas systems active.
Overview of the 8th Social Media Mining for Health Applications (#SMM4H) shared tasks at the AMIA 2023 Annual Symposium
Authors: Klein Ari Z , Banda Juan M , Guo Yuting , Schmidt Ana Lucia , Xu Dongfang , Flores Amaro Ivan , Rodriguez-Esteban Raul , Sarker Abeed , Gonzalez-Hernandez Graciela 
Published: January 2024

Abstract

Objective
The aim of the Social Media Mining for Health Applications (#SMM4H) shared tasks is to take a community-driven approach to address the natural language processing and machine learning challenges inherent to utilizing social media data for health informatics. In this paper, we present the annotated corpora, a technical summary of participants’ systems, and the performance results.

Methods
The eighth iteration of the #SMM4H shared tasks was hosted at the AMIA 2023 Annual Symposium and consisted of 5 tasks that represented various social media platforms (Twitter and Reddit), languages (English and Spanish), methods (binary classification, multi-class classification, extraction, and normalization), and topics (COVID-19, therapies, social anxiety disorder, and adverse drug events).

Results
In total, 29 teams registered, representing 17 countries. In general, the top-performing systems used deep neural network architectures based on pre-trained transformer models. In particular, the top-performing systems for the classification tasks were based on single models that were pre-trained on social media corpora.

Conclusion
To facilitate future work, the datasets—a total of 61 353 posts—will remain available by request, and the CodaLab sites will remain active for a post-evaluation phase.
Topic modeling on clinical social work notes for exploring social determinants of health factors
Authors: Sun Shenghuan , Zack Travis , Williams Christopher Y K , Sushil Madhumita , Butte Atul J 
Published: January 2024

Abstract

Objective
Existing research on social determinants of health (SDoH) predominantly focuses on physician notes and structured data within electronic medical records. This study posits that social work notes are an untapped, potentially rich source for SDoH information. We hypothesize that clinical notes recorded by social workers, whose role is to ameliorate social and economic factors, might provide a complementary information source of data on SDoH compared to physician notes, which primarily concentrate on medical diagnoses and treatments. We aimed to use word frequency analysis and topic modeling to identify prevalent terms and robust topics of discussion within a large cohort of social work notes including both outpatient and in-patient consultations.

Materials and methods
We retrieved a diverse, deidentified corpus of 0.95 million clinical social work notes from 181 644 patients at the University of California, San Francisco. We conducted word frequency analysis related to ICD-10 chapters to identify prevalent terms within the notes. We then applied Latent Dirichlet Allocation (LDA) topic modeling analysis to characterize this corpus and identify potential topics of discussion, which was further stratified by note types and disease groups.

Results
Word frequency analysis primarily identified medical-related terms associated with specific ICD10 chapters, though it also detected some subtle SDoH terms. In contrast, the LDA topic modeling analysis extracted 11 topics explicitly related to social determinants of health risk factors, such as financial status, abuse history, social support, risk of death, and mental health. The topic modeling approach effectively demonstrated variations between different types of social work notes and across patients with different types of diseases or conditions.

Discussion
Our findings highlight LDA topic modeling’s effectiveness in extracting SDoH-related themes and capturing variations in social work notes, demonstrating its potential for informing targeted interventions for at-risk populations.

Conclusion
Social work notes offer a wealth of unique and valuable information on an individual’s SDoH. These notes present consistent and meaningful topics of discussion that can be effectively analyzed and utilized to improve patient care and inform targeted interventions for at-risk populations.
Determination of Seven Human Milk Oligosaccharides (HMOs) in Infant Formula and Adult Nutritionals: First Action 2022.07
Authors: Bénet Thierry , Frei Nathalie , Spichtig Véronique , Cuany Denis , Austin Sean 
Published: January 2024

Abstract

Background
Human milk oligosaccharides (HMOs) are important components of breast milk and may be responsible for some of the benefits of breastfeeding, including resistance to infections and the development of a healthy gut microbiota. Selected HMOs are now available for addition to infant formula, and suitable methods to control the dosing rate are needed.

Objective
To develop and validate a suitable method for the analysis of HMOs in infant formula.

Method
A method was developed for the determination of seven human milk oligosaccharides (2′-fucosyllactose, 3-fucosyllactose, 3′-sialyllactose, 6′-sialyllactose (6′SL), 2′,3-difucosyllactose, lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT)) in infant formula and adult nutritionals. The oligosaccharides are labeled at their reducing end with 2-aminobenzamide, separated by liquid chromatography and detected using a fluorescence detector. Maltodextrins are enzymatically hydrolyzed before analysis to prevent potential interference; likewise, an optional β-galactosidase treatment can be used to remove β-galactooligosaccharides. Fructooligosaccharides or polydextrose do not generally interfere with the analysis.

Results
The method has been validated in a single laboratory on infant formula and adult nutritionals. The seven HMOs were spiked into eight matrixes at three or four spike levels, giving a total of 176 data points. Recoveries were in the range of 90.9–109% in all cases except at the lowest spike level in one matrix (elemental formula), where the LNT recovery was 113%, the LNnT recovery was 111%, and the 6′SL recovery was 121%. Relative repeatabilities (RSD(r)) were in the range of 0.1–4.2%. The performance is generally within the requirements outlined in the Standard Method Performance Requirements (SMPR®) published by AOAC INTERNATIONAL.

Conclusions
The method developed is suitable for the determination of seven HMOs in infant formula and demonstrated good performance during single-laboratory validation.

Highlights
A method has been developed that is suitable for the determination of seven HMOs in infant formula.
Relevance of Secondary Enrichment in the Detection of Salmonella spp. in Food Samples by qPCR According to DIN 10135
Authors: Codony Francesc , Agustí Gemma , Barreto Lina , Asensio Daniel 
Published: January 2024

Abstract

Background
When detecting Salmonella spp. in food samples, unlike with culture-based procedures where there are solid standards, PCR techniques are generally dominated by commercial solutions, often backed by the conformity of reference organizations, and based on rigorous validation studies. The few independent standards that exist are not subject to revision and improvement to the same extent as the manufacturer’s methods. Moreover, since commercial networks do not promote them, they are implemented less in everyday practice. The German standard DIN 10135 is an example of this. In this method, before PCR detection, a primary enrichment (16–20 h) followed by a secondary selective enrichment of at least 6 h is needed. Nevertheless, it allows the possibility of only applying the first step if evidence of their correct operation is provided.

Objective
To evaluate how necessary is the secondary enrichment for DIN 10135 standard.

Methods
Short and complete enrichment steps were compared in the context of the evaluation of the limit of detection for 11 types of food. Additionally, a blind assay was performed with 75 food samples.

Results
The data show that a simple primary enrichment may be sufficient and that the second selective enrichment with the tested matrixes would not be strictly essential. The blind study obtained a 98.6% of trueness and precision of 100%.

Conclusions
At least for the end consumer products, a secondary enrichment of 6 h is not necessary for all the products tested.

Highlights
In the context of the DIN 10135 standard, the primary enrichment (16–20 h, 37 ± 1°C) can be enough for detecting Salmonella spp.
Comparison of Six Aptamer-Aptamer Pairs on Rapid Detection of SARS-CoV-2 by Lateral Flow Assay
Authors: Çam Derin Dilek , Gültekin Enes , Gündüz Elif , Otlu Barış 
Published: January 2024

Abstract

Background
SARS-CoV-2 is a threat to humanity. Both the spike (S) protein and its receptor binding domain (sRBD) are extensively used for rapid detection. Although real-time reverse transcription polymerase chain reaction (rRT-PCR) is mostly used method for the molecular detection of SARS-CoV-2, rapid assays for antigenic detection are always needed. Lateral flow assays (LFAs) are the most commonly used tests for this purpose, and aptamers having stability and long shelf life are used as capture reagents.

Objective
This study aimed to develop the LFAs based on the aptamer pairs for the antigenic detection of SARS-CoV-2 with the naked eye.

Method
Gold nanoparticles (AuNPs) were used as labels, and six sandwich models by three different aptamers were prepared using 4 μM and 8 μM probes and two kinds of membranes for developing the LFAs.

Results
The 8 μM probe concentration and M2 membrane showed the best recognition of both the synthetic sRBD and SARS-CoV-2 coming from the naso/oropharingeal swabs by designed LFAs as 100% sensitivity and 93.3% specificity compared to the antibody-detecting LFAs.

Conclusions
Our developed strip assays based on aptamer pairs recognized the target directly in 5–6 min with the naked eye. It was also concluded that aptamer pairs, membrane types, assay buffers, and probe concentrations have a significant role in the detection of SARS-CoV-2 by LFAs.

Highlights
The detection of SARS-CoV-2 in clinical samples was demonstrated with the best aptamer pairs, sensitively and selectively among the designed six aptamer pairs for LFAs. Developed LFAs can be an alternative method to the conventional antibody-based LFAs for SARS-CoV-2 detection.
Stability Study Through Water Activity Measurements for Dispensed Powdered Raw Materials
Authors: Prada-Ramírez Harold A , Montes-Tamara Juan Pablo , Rico-Jimenez Eduardo A , Fonseca Juan Camilo 
Published: January 2024

Abstract

Background
Holding times for raw materials are relevant since they enable us to understand the allowable time that a raw material can be kept under ideal storage conditions before the start of the manufacturing process without its quality attributes being affected. The quantification of water activity can be used as an indicator of the microbiological, physicochemical, and organoleptic stability of a specimen, since low water activity retards autohydrolysis and microbiological growth.

Objective
The main purpose of this investigation was to test the stability of powdered raw materials for a maximum holding time of 8 days through water activity measurements. Thus microbiological, physicochemical, and organoleptic measurements were carried out in parallel and simultaneously to experimentally establish a relationship between the status of the water activity of processed raw materials and the microbiological, physicochemical, and organoleptic results.

Methods
The raw materials were stored for a maximum holding time of 8 days, in accordance with United States Pharmacopeia monographs. For all the raw materials tested, water activity measurements were performed using the dew point chilled-mirror method on days 0, 3, and 8. On days 0 and 8, microbiological, physicochemical, and organoleptic assessments were performed.

Results
It was established that under these storage conditions, the processed raw materials exhibited water activity below 0.60 during the entire holding time. However, there were statistically significant differences in water activity levels between days 0, 3, and 8 (ANOVA P &lt; 0.05). Despite observing statistically significant differences between days, the microbiological, physicochemical, and organoleptic features were within specification at those water activity levels below 0.60.

Conclusions
Water activity below 0.60 does not allow the growth of microorganisms, and the organoleptic and physicochemical features remain unperturbed. The results indicate that water activity can be used as an indicator of the microbiological load and chemical stability of the raw materials tested.

Highlights
This research provides evidence that corroborates that water activity status may be used as a reliable indicator for the microbiological burden and physicochemical features of pharmaceutical material during stability studies.
Effects of a second iron-dextran injection administered to piglets during lactation on differential gene expression in liver and duodenum at weaning
Authors: Pierce James L , Lyons J Wesley , Chevalier Tyler B , Lindemann Merlin D 
Published: January 2024

AbstractSix female littermate piglets were used in an experiment to evaluate the mRNA expression in tissues from piglets given one or two 1 mL injections of iron dextran (200 mg Fe/mL). All piglets in the litter were administered the first 1 mL injection &lt; 24 h after birth. On day 7, piglets were paired by weight (mean body weight = 1.72 ± 0.13 kg) and one piglet from each pair was randomly selected as control (CON) and the other received a second injection (+Fe). At weaning on day 22, each piglet was anesthetized, and samples of liver and duodenum were taken from the anesthetized piglets and preserved until mRNA extraction. differential gene expression data were analyzed with a fold change cutoff (FC) of |1.2| P &lt; 0.05. Pathway analysis was conducted with Z-score cutoff of P &lt; 0.05. In the duodenum 435 genes were significantly changed with a FC ≥ |1.2| P &lt; 0.05. In the duodenum, Claudin 1 and Claudin 2 were inversely affected by + Fe. Claudin 1 (CLDN1) plays a key role in cell-to-cell adhesion in the epithelial cell sheets and was upregulated (FC = 4.48, P = 0.0423). Claudin 2 (CLDN2) is expressed in cation leaky epithelia, especially during disease or inflammation and was downregulated (FC = −1.41, P = 0.0097). In the liver, 362 genes were expressed with a FC ≥ |1.2| P &lt; 0.05. The gene most affected by a second dose of 200 mg Fe was hepcidin antimicrobial peptide (HAMP) with a FC of 40.8. HAMP is a liver-produced hormone that is the main circulating regulator of Fe absorption and distribution across tissues. It also controls the major flows of Fe into plasma by promoting endocytosis and degradation of ferroportin (SLC4A1). This leads to the retention of Fe in Fe-exporting cells and decreased flow of Fe into plasma. Gene expression related to metabolic pathway changes in the duodenum and liver provides evidence for the improved feed conversion and growth rates in piglets given two iron injections preweaning with contemporary pigs in a companion study. In the duodenum, there is a downregulation of gene clusters associated with gluconeogenesis (P &lt; 0.05). Concurrently, there was a decrease in the mRNA expression of genes for enzymes required for urea production in the liver (P &lt; 0.05). These observations suggest that there may be less need for gluconeogenesis, and possibly less urea production from deaminated amino acids. The genomic and pathway analyses provided empirical evidence linking gene expression with phenotypic observations of piglet health and growth improvements.
Rehydration post-transport: duration of oral fluid therapy on behavior, biochemical measures of hydration, and health of neonatal dairy calves
Authors: Pempek Jessica A , England Zachary , Habing Gregory G , Niehaus Andrew 
Published: January 2024

Abstract
The objective of this study was to determine the impact of 0, 1, 2, or 3 d of oral electrolyte solutions (OES) following transport on calf behavior, biochemical measures of hydration, and subsequent health. Two cohorts of 60 Holstein bull calves ~3 to 7 d of age were included in this experiment. Calves (n = 30/treatment) were randomized to 1 of 4 treatments on arrival at a calf-raising facility: (1) 1-d OES, (2) 2-d OES, (3) 3-d OES, or (4) no OES (control). Calves were evaluated for signs of arthritis, depression, dehydration, diarrhea, fever, navel inflammation, and respiratory disease on arrival (day 0) and 1, 2, 3, and 7 d after arrival. Blood was obtained following each examination to assess biochemical measures of hydration, including serum electrolytes, glucose, hematocrit, lactate, pH, and serum total protein (STP). Calves were fitted with 3D accelerometers attached to the right hind leg along the metatarsus bone to continuously measure lying time. Linear regression models with Gaussian or Poisson link functions were used to test differences between treatments in blood parameters, as well as disease frequency and behavior, respectively. Calves spent the most time lying immediately post-transport (day 0); however, there was no effect of OES treatment on lying time. On arrival, 90% (95% CI: 84.6% to 95.4%) of calves had mild to moderate dehydration, and there was no significant difference in hydration status across treatments. Mildly dehydrated calves that received 1- and 2-d OES had higher STP concentration compared to the control. Moderately dehydrated calves that received 3- vs. 1-d OES had higher (101.4 vs. 93.7 mmol/L, respectively; P = 0.01) glucose concentration, and 3- vs. 2-d OES (101.4 vs. 96.2, respectively; P = 0.07) calves tended to have higher glucose concentration. The prevalence of failed transfer of passive immunity (STP &lt; 5.1 g/dL) and hypoglycemia (glucose &lt; 4.95 mmol/L) was 26.7% (18.6% to 34.7%) and 76.5% (68.7% to 84.2%), respectively. The frequency of moderate dehydration was lower for calves that received 2-d OES compared to the control (count ratio: 0.4; 0.2% to 0.8%; P = 0.009). These results underline the need for more research on rehydration strategies to help inform calf processing protocols. Future research should investigate preconditioning strategies to minimize the impact of marketing and transport on dairy calves. Continued nutritional-based research is also needed to better support calves’ recovery post-transport.