Search Results (2,657)

Two experiments were conducted to determine which part of the empty body of Boer × Saanen intact male kids can be used to predict the chemical composition of the whole body. In the first experiment, kids were fed ad libitum and slaughtered at 5, 10, and 15 kg body weight (BW). Eighteen animals were group-fed at three intake levels (ad libitum or restricted to 30% and 60% of the ad libitum level). When the ad libitum animal in the group reached 15 kg BW, all animals in the group were slaughtered. In the second experiment, kids were fed ad libitum and slaughtered at 15, 20, and 25 kg BW. Twenty-one animals were group-fed at three intake levels and slaughtered when the ad libitum animal within the group reached 25 kg BW. Analyzed body parts included head + feet, hide, organs, neck, shoulder, ribs, loin, leg, 9–11th ribs, and half carcass. Principal component and cluster analyses showed that the neck, 9–11th ribs, and loin had the highest frequency of grouping with the empty body. These body parts were used to develop prediction models for estimating body composition. The neck, loin, and 9–11th ribs accurately and precisely predicted the dry matter, ash, fat, protein, and energy body composition of goats, with most models also incorporating BW as a predictor variable. The equations showed root mean squared error (RMSE) lower than 13.5% and a concordance correlation coefficient (CCC) greater than 0.84. Fat and protein concentrations in the loin and neck were also reliable predictors of empty body energy composition (RMSE = 2.9% of mean and concordance correlation coefficient = 0.93). Removing the loin and 9–11th ribs could reduce the carcass retail price. Using the neck to estimate body composition in growing Boer × Saanen goats provides a valuable alternative for nutrition studies, given its low commercial value. Full article

Background: The increasing integration of AI in chest X-ray evaluation holds promise for enhancing diagnostic accuracy and optimizing clinical workflows. However, understanding its performance in real-world clinical settings is essential. Objectives: In this study, we evaluated the sensitivity (Se) and specificity (Sp) of an AI-based software (Arterys MICA v29.4.0) alongside a radiology resident in interpreting chest X-rays referred from the emergency department (ED), using a senior radiologist’s assessment as the gold standard (GS). We assessed the concordance between the AI system and the resident, noted the frequency of doubtful cases for each category, identified how many were considered positive by the GS, and assessed variables that AI was not trained to detect. Methods: We conducted a retrospective observational study analyzing chest X-rays from a sample of 784 patients referred from the ED at our hospital. The AI system was trained to detect five categorical variables—pulmonary nodule, pulmonary opacity, pleural effusion, pneumothorax, and fracture—and assign each a confidence label (“positive”, “doubtful”, or “negative”). Results: Sensitivity in detecting fractures and pneumothorax was high (100%) for both AI and the resident, moderate for pulmonary opacity (AI = 76%, resident = 71%), and acceptable for pleural effusion (AI = 60%, resident = 67%), with negative predictive values (NPV) above 95% and areas under the curve (AUC) exceeding 0.8. The resident showed moderate sensitivity (75%) for pulmonary nodules, while AI’s sensitivity was low (33%). AI assigned a “doubtful” label to some diagnoses, most of which were deemed negative by the GS; the resident expressed doubt less frequently. The Kappa coefficient between the resident and AI was fair (0.3) across most categories, except for pleural effusion, where concordance was moderate (0.5). Our study highlighted additional findings not detected by AI, including 16% prevalence of mediastinal abnormalities, 20% surgical materials, and 20% other pulmonary findings. Conclusions: Although AI demonstrated utility in identifying most primary findings—except for pulmonary nodules—its high NPV suggests it may be valuable for screening. Further training of the AI software and broadening its scope to identify additional findings could enhance its detection capabilities and increase its applicability in clinical practice. Full article

The genus Vitis, known for its economically important fruit—grape—is divided into three geographical groups, American, East Asian, and Eurasian, along with a hybrid group. However, previous studies on grape phylogeny using chloroplast genomes have been hindered by limited sample sizes and inconsistent methodologies, resulting in inaccuracies. In this study, we employed the GetOrganelle software with consistent parameters to assemble the chloroplast genomes of 21 grape cultivars, ensuring comprehensive representation across four distinct groups. A comparative analysis of the 21 grape cultivars revealed structural variation, showing chloroplast genome sizes ranging from 160,813 bp to 161,275 bp. In 21 Vitis cultivars, genome annotation revealed 134 to 136 genes, comprising 89 to 91 protein-coding genes (PCGs), 37 tRNAs, and 8 rRNAs. Our observations have pinpointed specific occurrences of contraction and expansion phenomena at the interfaces between inverted repeat (IR) regions and single-copy (SC) regions, particularly in the vicinity of the rpl2, ycf1, ndhF, and trnN genes. Meanwhile, a total of 193 to 198 SSRs were identified in chloroplast genomes. The diversification pattern of chloroplast genomes exhibited strong concordance with the phylogenetic relationships of the Euvitis subgenera. Phylogenetic analysis based on conserved chloroplast genome strongly clustered the grape varieties according to their geographical origins. In conclusion, these findings enhance our understanding of chloroplast genome variation in Vitis populations and have important implications for cultivar selection, breeding, and conservation efforts. Full article

Background: The early exposure of nutrients during pubertal mammary gland development may reduce the risk of developing breast cancer later in life. Anticancer n-3 polyunsaturated fatty acids (n-3 PUFA) are shown to modulate pubertal mammary gland development; however, the mechanisms of action remain unclear. Prior work focused on effects at the whole tissue level, and little is known at the cellular level, such as at the level of mammary epithelial cells (MECs), which are implicated in cancer development. Methods: This pilot study examined the effects of lifelong n-3 PUFA exposure on the transcriptome by RNA-Seq in the isolated MECs of pubertal (6–8-week-old) female fat-1 transgenic mice capable of de novo n-3 PUFA synthesis. edgeR and DESeq2 were used separately for the differential expression analysis of RNA sequencing data followed by the Benjamani–Hochberg procedure for multiple testing correction. Results: Nine genes were found concordant and significantly different (p ≤ 0.05) by both the DESeq2 and edgeR methods. These genes were associated with multiple pathways, suggesting that n-3 PUFA stimulates estrogen-related signaling (Mlltl0, Galr3, and Nrip1) and a glycolytic profile (Soga1, Pdpr, and Uso1) while offering protective effects for immune and DNA damage responses (Glpd1, Garre1, and Rpa1) in MECs during puberty. Conclusions: This pilot study highlights the utility of RNA-Seq to better understanding the mechanistic effects of specific nutrients such as n-3 PUFA in a cell-specific manner. Thus, further studies are warranted to investigate the cell-specific mechanisms by which n-3 PUFA influences pubertal mammary gland development and breast cancer risk later in life. Full article

Seed germination is a fundamental process in plant reproduction, and it involves a series of complex physiological mechanisms. The germination rate of Astragalus mongholicus (AM) seeds is significantly lower under natural conditions. To investigate the key genes associated with AM seed germination, seeds from AM plants were collected at 0, 12, 24, and 48 h for a transcriptomic analysis, weighted gene co-expression network analysis (WGCNA), and machine learning (ML) analysis. The primary pathways involved in AM seed germination include plant-pathogen interactions and plant hormone signaling. Four key genes were identified through the WGCNA and ML: Cluster-28,554.0, FAS4, T10O24.10, and EPSIN2. These findings were validated using real-time quantitative reverse transcription PCR (qRT-PCR), and results from RNA sequencing demonstrated a high degree of concordance. This study reveals, for the first time, the key genes related to AM seed germination, providing potential gene targets for further research. The discovery of N4-acetylcysteine (ac4C) modification during seed germination not only enhances our understanding of plant ac4C but also offers valuable insights for future functional research and application exploration. Full article

The analytical performance of the new Aspergillus Galactomannan Ag VirCLIA^® mono-test (Vircell S.L.) was compared to the Platelia™ Aspergillus Ag ELISA assay (Bio-Rad). Prospective serum and bronchoalveolar lavage (BAL) samples from patients at risk of invasive aspergillosis (IA) were tested using both the Aspergillus Galactomannan Ag VirCLIA^® mono-test and the Platelia™ Aspergillus Ag ELISA assay. Concordance, sensitivity, specificity, and positive and negative predictive values were calculated using the manufacturer-recommended cutoff levels. Receiver operating characteristic (ROC) analysis and the Youden index were performed to determine the optimal cutoff. A total of 187 serum samples and 73 BAL samples were analyzed with both assays. The concordance between the Aspergillus Galactomannan Ag VirCLIA^® mono-test and the Platelia™ Aspergillus Ag ELISA assay was 87.8%, with a Cohen’s kappa of 0.75. The sensitivity and specificity of the Aspergillus Galactomannan Ag VirCLIA^® mono-test were 78.6% and 96.2%, respectively, with positive and negative predictive values of 94.8% and 83.3%. The ROC curve for the Aspergillus Galactomannan Ag VirCLIA^® mono-test demonstrated an area under the curve (AUC) of 0.87, and the Youden index at the manufacturer’s established cutoff was 0.73. This new Aspergillus Galactomannan Ag VirCLIA^® mono-test exhibited adequate analytical and clinical performance, showing good correlation with the Platelia™ Aspergillus Ag ELISA assay. The single-sample, semi-automated test is user-friendly, allowing small laboratories to perform the test on demand without the need for batch evaluations, providing a useful solution for timely diagnostic support for clinicians. Full article

Background: The selection of the best donor for each specific patient is crucial for the success of allogeneic hematopoietic stem cell transplantation (HSCT). However, there is debate on the choice of the best donor when multiple suitable donors exist. Methods: By using own data from two transplant centers, we have developed a calculator able to provide the patients’ 2-year overall survival (OS) associated with each of the potential donor options during the selection process, in order to support the transplant physician during the choice. Data on 737 HSCTs with HLA-identical siblings, and unrelated or related haploidentical donors from January 2010 to July 2022 have been retrospectively obtained. Results: Patients’ age, disease, comorbidity index, and donor type were found to be significant variables able to predict the outcome with robustness (concordance index: 0.677). Estimates are provided within an example in the text showing outcomes with four donor options for a specific patient. Conclusions: We present the prototype of a tool supporting the selection of the best donor, guiding transplant physicians during the delicate process of donor selection before HSCT. This approach relies on real data from the centers, reflecting their local clinical experience. Improvements are underway with a larger, ongoing multicenter study. Full article

Background/Objectives: Colorectal cancer (CRC) is the third leading cause of cancer death globally, with rising incidence. The immunohistochemistry (IHC) for mismatch repair (MMR) proteins is the first technique used in routine practice to evaluate an MMR status. Microsatellite instability (MSI) may be tested in case of doubt during IHC staining. This study introduces a novel high-resolution melt (HRM) protocol for MSI detection and compares it with traditional fragment length analysis (FLA) via capillary electrophoresis. Methods: A total of 100 formalin-fixed and paraffin-embedded CRC specimens were analyzed using two distinct protocols: one based on FLA (TrueMark MSI Assay kit) and another one based on HRM (AmoyDx^® Microsatellite Instability Detection Kit). Results: Overall, 68 (68.0%) of the cases were MSS, and 32 (32.0%) were MSI-H. HRM analysis was first successfully carried out in all the cases. A perfect concordance in MSI evaluation between HRM and FLA was observed. HRM showed slightly shorter hands-on time and turnaround time. Conclusions: We provided evidence of the validity of this new HRM approach in determining the MSI status of colorectal carcinomas. Full article

Background: Fanconi syndrome is a disorder of renal proximal tubule transport characterized by metabolic acidosis, amino aciduria, glucosuria, and phosphaturia. There are acquired and hereditary forms of this disorder. A late-onset form of Fanconi syndrome in Basenjis was first described in 1976 and is now recognized as an inherited disease in these dogs. In part because of the late onset of disease signs, the disorder has not been eradicated from the breed by selective mating. A study was therefore undertaken to identify the molecular genetic basis of the disease so that dogs could be screened prior to breeding in order to avoid generating affected offspring. Methods: Linkage analysis within a large family of Basenjis that included both affected and unaffected individuals was performed to localize the causative variant within the genome. Significant linkage was identified between chromosome 3 (CFA3) makers and the disease phenotype. Fine mapping restricted the region to a 2.7 Mb section of CFA3. A whole genome sequence of a Basenji affected with Fanconi syndrome was generated, and the sequence data were examined for the presence of potentially deleterious homozygous variants within the mapped region. Results: A homozygous 317 bp deletion was identified in the last exon of FAN1 of the proband. 78 Basenjis of known disease status were genotyped for the deletion variant. Among these dogs, there was almost complete concordance between genotype and phenotype. The only exception was one dog that was homozygous for the deletion variant but did not exhibit signs of Fanconi syndrome. Conclusions: These data indicate that the disorder is very likely the result of FAN1 deficiency. The mechanism by which this deficiency causes the disease signs remains to be elucidated. FAN1 has endonuclease and exonuclease activity that catalyzes incisions in regions of double-stranded DNA containing interstrand crosslinks. FAN1 inactivation may cause Fanconi syndrome in Basenjis by sensitization of kidney proximal tubule cells to toxin-mediated DNA crosslinking, resulting in the accumulation of genomic and mitochondrial DNA damage in the kidney. Differential exposure to environmental toxins that promote DNA crosslink formation may explain the wide age-at-onset variability for the disorder in Basenjis. Full article

Background/objectives:To date, no studies have evaluated Chat Generative Pre-Trained Transformer (ChatGPT) as a large language model chatbot in optical applications for digestive endoscopy images. This study aimed to weigh the performance of ChatGPT-4 in assessing bowel preparation (BP) quality for colonoscopy. Methods: ChatGPT-4 analysed 663 anonymised endoscopic images, scoring each according to the Boston BP scale (BBPS). Expert physicians scored the same images subsequently. Results: ChatGPT-4 deemed 369 frames (62.9%) to be adequately prepared (i.e., BBPS > 1) compared to 524 frames (89.3%) assessed by human assessors. The agreement was slight (κ: 0.099, p = 0.0001). The raw human BBPS score was higher at 3 (2–3) than that of ChatGPT-4 at 2 (1–3), demonstrating moderate concordance (W: 0.554, p = 0.036). Conclusions: ChatGPT-4 demonstrates some potential in assessing BP on colonoscopy images, but further refinement is still needed. Full article

Salmonella spp. are known pathogens in fish, with their presence potentially resulting from the contamination of the aquatic environment or improper handling. Accurate bacterial identification is crucial across various fields, including medicine, microbiology, and the food industry, and thus a range of techniques are available for this purpose. In this study, Salmonella spp. and other hydrogen sulphide-positive bacteria were investigated in the digestive contents of fish destined for consumption from the Atlantic area of Macaronesia. Two identification techniques were compared: the traditional API method and the MALDI-TOF MS technique. For the identification of Salmonella spp. carriers, 59 samples were processed following ISO 6579–1:2017. A total of 47 strains of Gram-negative bacilli were obtained. No Salmonella spp. isolates were detected. The most frequent genus was Enterobacter (76.50%), followed by Shewanella (10.63%). The MALDI-TOF MS technique showed a high concordance with the API technique, with 72.34% concordance at the species level. Both techniques demonstrated a high degree of concordance in the identification of Enterobacter cloacae, with 87.23% genus-level concordance and 12.76% non-concordant identifications. This study highlights the limitations of the API technique and the speed and precision of MALDI-TOF MS. The identified bacteria could pose a health risk to humans. Full article

Background/Objectives: Directed acyclic graphs (DAGs) inform the epidemiologic statistical modeling confounders to determine close to true causal relationships in a study context. They inform the inclusion of the predictive model variables that affect the causal relationship. Non-small cell lung cancer (NSCLC) is frequently diagnosed, aggressive, and the second leading cause of cancer deaths in the United States. Determining factors affecting both the guideline-concordant treatment receipt and survival outcomes for early-stage lung cancer will help inform future statistical models aiming to achieve a close to true causal relationship. Methods: Peer-reviewed original research published during 2002–2023 was identified through PubMed, Embase, Web of Sciences, Clinical trials registry, and the gray literature. DAGitty version 3.1, an online software program, developed implied DAGs and integrated DAG graphics. The evidence synthesis for constructing directed acyclic graphs (ESC-DAGs) protocol was utilized to guide DAG development. The conceptual models utilized were Andersen and Aday for factors affecting treatment receipt and Shi and Steven for survival outcome factors. Results: A total of 36 studies were included in the DAG synthesis out of 9421 retrieved across databases. Eight studies served in the synthesis of treatment receipt DAG, while 28 studies were used for the survival outcomes DAG. There were 10 causal paths and 13 covariates for treatment receipt and 2 causal pathways and 32 covariates for survival outcomes. Conclusions: There are very few studies reporting on factors affecting early-stage NSCLC guideline-concordant care receipt compared to factors affecting its survival outcomes in the past two decades of original research. Future investigations can utilize data extracted in the current study to develop a meta-analysis informing effect size. Full article

Antimicrobial resistance (AMR) poses a significant global health challenge affecting food safety and development. Residues of antibiotics in food from animal sources, particularly milk, contribute to the development and spread of AMR, alter intestinal microbiota, and potentially lead to allergies, serious health conditions, and environmental and technological problems within the dairy industry. Therefore, this study investigated the residue levels of veterinary drugs from β-lactam antibiotics and tetracyclines in milk and milk products and assessed human health risks. Two hundred milk and milk product samples (pasteurized milk, sterile milk, soft white cheese, and processed cheese, 50 each) were collected from different hospitals in the State of Kuwait and screened for antibiotic residues using a microbial inhibition assay (Delvotest SP-NT) and high-performance liquid chromatography (HPLC). Delvotest SP-NT and HPLC analyses showed that 30, 28, 26, and 24% of the pasteurized milk, sterilized milk, white soft cheese, and processed cheese samples tested positive for antibiotic residues. Forty-eight milk and cheese samples were confirmed as positive by both methods, and six samples initially found to be negative by Delvotest SP-NT were confirmed as positive by HPLC. Multi-antibiotic residues were detected in five samples by using HPLC. The kappa coefficient (0.921; p < 0.0001) revealed complete concordance between the HPLC and Delvotest SP-NT results. Ampicillin was the most abundant residue in the positive samples (31.48%), ranging from 2.44 to 3.89 μg/L, with an overall mean concentration of 3.492 ± 0.094 μg/L, followed by tetracycline and oxytetracycline (27.78% each), ranging from 54.13 to 220.3 μg/L and from 41.55 to 160.7 μg/L, with mean concentrations of 129.477 ± 14.22 and 91.86 ± 9.92 μg/L, respectively. The amoxicillin levels in the samples (12/54; 22.22%) ranged from 3.11 to 5.5 μg/L, with an overall mean concentration of 3.685 ± 0.186 μg/L. The maximum concentrations of ampicillin, amoxicillin, and tetracycline were detected in processed cheese with mean concentrations of 3.89 ± 0.28 µg/L, 3.95 ± 0.15 µg/L, and 170.3 ± 0.27 µg/L, respectively. Pasteurized milk contained the maximum concentrations of oxytetracycline, with a mean concentration of 120.45 ± 0.25 µg/L. The tetracycline residues exceeded the standard maximum residue limits (MRLs; 100 µg/L) in 6% of both pasteurized and sterilized milk samples, and in 4% of processed cheese. Additionally, the oxytetracycline levels in pasteurized milk (6%) and amoxicillin levels in processed cheese (2%) were higher than the permitted MRLs (100 µg/L and 4 µg/L, respectively). Furthermore, the antibiotic residues detected in 12.5% (25/200) of the samples were close to standard permissible MRL limits for ampicillin (5%), amoxicillin and oxytetracycline (3% each), and tetracycline (1.5%). Hazard quotients, which compare the standard acceptable daily intake (ADI) to the estimated daily exposure (EDI), indicated that the overall risk associated with antibiotic residues in these dairy products is low. The EDI was lower than the ADI for the tested antibiotics, indicating an elevated safety margin. While the overall hazard quotients are low, the potential for the development of antibiotic resistance due to long-term exposure to low levels of antibiotics should be considered. Hence, strict regulations and enforcement are necessary to prevent excessive residue levels and to promote responsible antibiotic use in dairy production. Regular monitoring of antibiotic residues in dairy products is essential for ensuring consumer safety. Full article

Background: Socioeconomic deprivation has been associated with higher lung cancer risk and mortality in non-Veteran populations. However, the impact of socioeconomic deprivation on outcomes for non-small cell lung cancer (NSCLC) in an integrated and equal-access healthcare system, such as the Veterans Health Administration (VHA), remains unclear. Hence, we investigated the impact of area-level socioeconomic deprivation on access to care and postoperative outcomes for early-stage NSCLC in United States Veterans. Methods: We conducted a retrospective cohort study of patients with clinical stage I NSCLC receiving surgical treatment in the VHA between 1 October 2006 and 30 September 2016. A total of 9704 Veterans were included in the study and assigned an area deprivation index (ADI) score, a measure of socioeconomic deprivation incorporating multiple poverty, education, housing, and employment indicators. We used multivariable analyses to evaluate the relationship between ADI and postoperative outcomes as well as adherence to guideline-concordant care quality measures (QMs) for stage I NSCLC in the preoperative (positron emission tomography [PET] imaging, appropriate smoking management, pulmonary function testing [PFT], and timely surgery [≤12 weeks after diagnosis]) and postoperative periods (appropriate surveillance imaging, smoking management, and oncology referral). Results: Compared to Veterans with low socioeconomic deprivation (ADI ≤ 50), those residing in areas with high socioeconomic deprivation (ADI > 75) were less likely to have timely surgery (multivariable-adjusted odds ratio [aOR] 0.832, 95% confidence interval [CI] 0.732–0.945) and receive PET imaging (aOR 0.592, 95% CI 0.502–0.698) and PFT (aOR 0.816, 95% CI 0.694–0.959) prior to surgery. In the postoperative period, Veterans with high socioeconomic deprivation had an increased risk of 30-day readmission (aOR 1.380, 95% CI 1.103–1.726) and decreased odds of meeting all postoperative care QMs (aOR 0.856, 95% CI 0.750–0.978) compared to those with low socioeconomic deprivation. There was no association between ADI and overall survival (adjusted hazard ratio [aHR] 0.984, 95% CI 0.911–1.062) or cumulative incidence of cancer recurrence (aHR 1.047, 95% CI 0.930–1.179). Conclusions: Our results suggest that Veterans with high socioeconomic deprivation have suboptimal adherence to care QMs for stage I NSCLC yet do not have inferior long-term outcomes after curative-intent resection. Collectively, these findings demonstrate the efficacy of an integrated, equal-access healthcare system in mitigating disparities in lung cancer survival that are frequently present in other populations. Future VHA policies should continue to target increasing adherence to QMs and reducing postoperative readmission for socioeconomically disadvantaged Veterans with early-stage NSCLC. Full article

The InVEST model, with its ability to perform spatial visualization and quantification, is an important tool for mapping ecosystem services. However, the spatial accuracy and simulating performance of the model are deeply influenced by the land use parameter, which often relies on the accuracy of land use/cover data. To address this issue, we propose a novel method for optimizing the land use parameter of the InVEST model based on the vegetation–impervious surface–soil (V–I–S) model and a machine learning algorithm. The optimized model is called Sub-InVEST, and it improves the performance of assessing ecosystem services on a sub-pixel scale. The conceptual steps are (i) extracting the V–I–S fraction of remote sensing images based on the spectral unmixing method; (ii) determining the mapping relationship of the V–I–S fraction between land use/cover type using a machine learning algorithm and field observation data; (iii) inputting the V–I–S fraction into the original model instead of the land use/cover parameter of the InVEST model. To evaluate the performance and spatial accuracy of the Sub-InVEST model, we employed the habitat quality module of InVEST and multi-source remote sensing data, which were applied to acquire Sub-InVEST and estimate the habitat quality of central Guangzhou city from 2000 to 2020 with the help of the LSMA and ISODATA methods. The experimental results showed that the Sub-InVEST model is robust in assessing ecosystem services in sets of complex ground scenes. The spatial distribution of the habitat quality of both models revealed a consistent increasing trend from the southwest to the northeast. Meanwhile, linear regression analyses observed a robust correlation and consistent linear trends, with R² values of 0.41, 0.35, 0.42, 0.39, and 0.47 for the years 2000, 2005, 2010, 2015, and 2020, respectively. Compared with the original model, Sub-InVEST had a more favorable performance in estimating habitat quality in central Guangzhou. The spatial depictions and numerical distribution of the results of the Sub-InVSET model manifest greater detail and better concordance with remote sensing imagery and show a more seamless density curve and a substantially enhanced probability distribution across interval ranges. Full article