Miracle-dz/UniFAR-FTUs huggingface dataset:
Missing Data in Sea Turtle Population Monitoring: A Bayesian Statistical Framework Accounting for Incomplete Sampling

Monitoring how populations respond to sustained conservation measures is essential to detect changes in their population status and determine the effectiveness of any interventions. In the case of sea turtles, their populations are difficult to assess because of their complicated life histories. Ground-derived clutch counts are most often used as an index of population size for sea turtles; however, data are often incomplete with varying sampling intensity within and among sites and seasons. To address these issues, we: (1) develop a Bayesian statistical modelling framework that can be used to account for sampling uncertainties in a robust probabilistic manner within a given site and season; and (2) apply this to a previously unpublished long-term sea turtle dataset (n = 17 years) collated for the Republic of the Congo, which hosts two sympatrically nesting species of sea turtle (leatherback turtle [Dermochelys coriacea] and olive ridley turtle [Lepidochelys olivacea]). The results of this analysis suggest that leatherback turtle nesting levels dropped initially and then settled into quasi-cyclical levels of interannual variability, with an average of 573 (mean, 95% prediction interval: 554–626) clutches laid annually between 2012 and 2017. In contrast, nesting abundance for olive ridley turtles has increased more recently, with an average of 1,087 (mean, 95% prediction interval: 1,057–1,153) clutches laid annually between 2012 and 2017. These findings highlight the regional and global importance of this rookery with the Republic of the Congo, hosting the second largest documented populations of olive ridley and the third largest for leatherback turtles in Central Africa; and the fourth largest non-arribada olive ridley rookery globally. Furthermore, whilst the results show that Congo’s single marine and coastal national park provides protection for over half of sea turtle clutches laid in the country, there is scope for further protection along the coast. Although large parts of the African coastline remain to be adequately monitored, the modelling approach used here will be invaluable to inform future status assessments for sea turtles given that most datasets are temporally and spatially fragmented.
Impact of Critical Success Factors on Project Success Through the Mediation of Knowledge Creation

Several factors affect health project success. This research aims to examine the impact of critical success factors on health project success and show how the essential factors of success interact with knowledge creation to impact health project success. The self-administered questionnaire was distributed to collect data from 246 managers, supervisors and zonal supervisors of DHQ hospital Attock and PIMS hospital Islamabad. The analysis was done using Smart PLS to understand the effect of exogenous variables over endogenous variables and the impact of mediating variables between two constructs. The results show that all critical success factors (MGTRF, DRF, CRF, PMRF, CLRF) are significantly affecting project success, in addition, tacit knowledge creation mediate the association between critical success factors and project success. In contrast, explicit knowledge creation does not mediate the relationship between critical success factors and project success. This study intends to expand the theoretical understanding of process improvement by providing practical insights into the impact of strategies used by project managers to develop new knowledge by capturing explicit and implicit information. This study also reinforces past findings and increases awareness about using knowledge creation to gain a competitive advantage in the health sector.
Valuing the “Burden” and Impact of Rare Diseases: A Scoping Review

Introduction: Rare diseases (RDs) are a severe, chronic, degenerative and often life-threatening group of conditions affecting more than 30 million people in Europe. Their impact is often underreported and ranges from psychological and physical symptoms seriously compromising quality of life. There is then a need to consolidate knowledge on the economic, social, and quality of life impacts of rare diseases. Methods: This scoping review is the result of 9 qualitative interviews with experts and a literature search on Cost-of-Illness (COI) studies and quality of life (QoL) studies following the PRISMA methodology. Grey literature was also included to complement findings. Results. 63 COI studies were retrieved, covering 42 diseases and a vast majority of them using a prevalence-based approach (94%). All studies included medical costs, while 60% included non-medical costs, 68% productivity losses and 43% informal care costs. 56 studies on QoL were retrieved, mostly from Europe, with 30 different measurement tools. Grey literature included surveys from the pharmaceutical industry and patient organisations. Discussion: The majority of studies evaluating the impact of RDs on the individual and society use the COI approach, mostly from a societal perspective. Studies often vary in scope, making them difficult to consolidate or compare results. While medical costs and productivity losses are consistently included, QoL aspects are rarely considered in COI and are usually measured through generic tools. Conclusion: A comprehensive study on impact of rare disease across countries in Europe is lacking. Existing studies are heterogeneous in their scope and methodology and often lack a holistic picture of the impact of rare. Consensus on standards and methodology across countries and diseases is then needed. Studies that consider a holistic approach are often conducted by pharmaceutical companies and patient organisations exploring a specific disease area but are not necessarily visible in the literature and could benefit from the sharing of standards and best practices.
Green Human Resource Management and Sustainable Performance With the Mediating Role of Green Innovation: A Perspective of New Technological Era

The purpose of this study is to investigate the relationship between green human resource management bundle practices and green innovation and their impact on sustainability performance as measured by the Triple Bottom Lines (i.e., environmental, social, and economic performance). It is decided to use a quantitative approach in order to collect data from 335 small- and medium-sized (SMEs) businesses operating in the Kingdom of Saudi Arabia, through a customized survey. Structure equation modeling was applied through smart PLS to analyze the collected data. Results show that green human resource management bundle practices have a positive and significant impact on the sustainable performance of SMEs. Furthermore, results indicate that green innovation has a significant impact on sustainable performance and green innovation partially mediates the relationship between green human resource practices and sustainable performance of SMEs. This study demonstrates that the implementation of GI by firms can be enhanced through the use of GHRM, which, in turn, would enhance the firms’ sustainability. Additionally, this study both confirms and enhances the traditional understanding. The study also depicts that environmental management practices in the human resource and innovation sectors can result in greater sustainability.
Contribution of HLA and KIR Alleles to Systemic Sclerosis Susceptibility and Immunological and Clinical Disease Subtypes

Systemic sclerosis (SSc) is an autoinflammatory, fibrotic condition of unknown aetiology. The presence of detectable autoantibodies against diverse nuclear antigens, as well as strong HLA associations with disease, suggest autoimmune involvement, however the links between endogenous and exogenous risk factors and SSc pathology remain undetermined. We have conducted a genetic analysis of HLA inheritance in two independent and meta-analysed cohorts of 1,465 SSc cases and 13,273 controls, including stratified association analyses in clinical and autoantibody positive subgroups of disease. Additionally, we have used patient genotypes to impute gene dosages across the KIR locus, encoding paired activating and inhibitory lymphocyte receptors for Class I HLA ligands, to conduct the largest analysis of KIR-HLA epistatic interactions in SSc to date. We confirm previous Class II HLA associations with SSc risk and report a new Class I association with haplotype HLA-B*44:03-HLA-C*16:01 at genome-wide significance (GWS). We further report statistically significant HLA associations with clinical and serological subtypes of disease through direct case-case comparison, and report a new association of HLA-DRB1*15:01, previously shown to bind topoisomerase-1 derived peptides, with anti-topoisomerase (ATA) positive disease. Finally, we identify genetic epistasis between KIRs and HLA class I ligands, suggesting genetic modulation of lymphocyte activation may further contribute to an individual’s underlying disease risk. Taken together, these findings support future functional investigation into endogenous immunological and environmental stimuli for disrupted immune tolerance in SSc.
Atlantic Salmon (Salmo salar) Performance Fed Low Trophic Ingredients in a Fish Meal and Fish Oil Free Diet

To evolve fish farming in an eco-efficient way, feed production must become less dependent on forage fish-based ingredients and make more use of low trophic level organisms, including microalgae, higher plants, as filter feeding organisms and other ingredients with low competition to established food value chains. Diets nearly free of fish meal and fish oil are not a novelty but are often composed of complex mixtures, containing supplements to meet the farmed animal’s nutritional requirements. Sustaining a growing aquaculture production, maintaining at the same time fish health, welfare, and profitability, and meeting strict environmental and food safety demands, is challenging and requires new technologies, great investments, and more knowledge. A benchmarking feeding trial was performed to demonstrate the main effects of four low trophic raw materials on Atlantic salmon (Salmo salar) growth, metabolism, skin health and fillet quality. To this end, a diet was produced to contain commercially relevant levels of fresh high quality organic FM and FO and was used as a control in the trial (FMFO). Heterotrophically produced Schizochytrium limacinum biomass was used to replace organic FO (HM diet). Spray dried cell wall disrupted biomass of the phototrophically cultured diatom Phaeodactylum tricornutum replaced partly FM and FO (PM diet). Black soldier fly (Hermetia illucens) larvae meal and tunicate (Ciona intestinalis) meal, were used to produce the diets BSFL and TM, respectively, replacing large parts of FM as compared to the FMFO. A fifth test diet was produced combining all test raw materials and removing all FM and FO (0FM0FO diet). All test ingredients were well accepted sustaining high growth rates (TGC values near 4) and feed efficiency (FCR values below 0.9) in salmon showing good gut health and normal metabolic responses. However, none of the treatments reached the growth performance of FMFO. Additional differences between test and control treatments were identified in dietary nutrient apparent digestibility, fish biometrics, blood metabolites and fillet and skin composition. Extensive raw material and dietary chemical characterisation was performed to provide insight on potential shortcomings in the novel low trophic level ingredients which can possibly be overcome combining complementary raw materials.
Carbocisteine as a Modulator of Nrf2/HO-1 and NFκB Interplay in Rats: New Inspiration for the Revival of an Old Drug for Treating Ulcerative Colitis

Ulcerative colitis (UC), an inflammatory bowel disease, is a chronic condition of a multifaceted pathophysiology. The incidence of UC is increasing internationally. The current therapies for UC lack relative effectiveness and are associated with adverse effects. Therefore, novel therapeutic options should be developed. It has been well documented that modulating the Nrf2/NFκB is a promising therapeutic target in inflammation. Carbocisteine is a mucoregulatory medication and its efficacy in COPD was found to be more closely related to its antioxidant and anti-inflammatory properties. Carbocisteine has not yet been examined for the management of UC. Hence, our approach was to investigate the potential coloprotective role of carbocisteine in acetic acid-induced colitis in rats. Our results revealed that carbocisteine improved colon histology and macroscopic features and subdued the disease activity as well. Additionally, carbocisteine attenuated colon shortening and augmented colon antioxidant defense mechanisms via upregulating catalase and HO-1 enzymes. The myeloperoxidase activity was suppressed indicating inhibition of the neutrophil infiltration and activation. Consistent with these findings, carbocisteine boosted Nrf2 expression along with NFκB inactivation. Consequently, carbocisteine downregulated the proinflammatory cytokines IL-6 and TNF-α and upregulated the anti-inflammatory cytokine IL-10. Concomitant to these protective roles, carbocisteine displayed anti-apoptotic properties as revealed by the reduction in the Bax: BCL-2 ratio. In conclusion, carbocisteine inhibited oxidative stress, inflammatory response, and apoptosis in acetic acid-induced UC by modulating the Nrf2/HO-1 and NFκB interplay in rats. Therefore, the current study provides a potential basis for repurposing a safe and a commonly used mucoregulator for the treatment of UC.
CRISPR-Cas9-Based Technology for Studying Enteric Virus Infection

Enteric viruses, including numerous viruses that initiate infection in enteric canal, are recognized as important agents that cause wide spectrum of illnesses in humans, depending on the virus type. They are mainly transmitted by fecal-oral route with several vector such as contaminated water or food. Infections by enteric viruses, such as noroviruses and rotaviruses, frequently cause widespread acute gastroenteritis, leading to significant health and economic burdens and therefore remain a public health concern. Like other viruses, enteric viruses ‘‘hijack’’ certain host factors (so called pro-viral factors) for replication in infected cells, while escaping the host defense system by antagonizing host anti-viral factors. Identification(s) of these factors is needed to better understand the molecular mechanisms underlying viral replication and pathogenicity, which will aid the development of efficient antiviral strategies. Recently, the advancement of genome-editing technology, especially the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system, has precipitated numerous breakthroughs across the field of virology, including enteric virus research. For instance, unbiased genome-wide screening employing the CRISPR-Cas9 system has successfully identified a number of previously unrecognized host factors associated with infection by clinically relevant enteric viruses. In this review, we briefly introduce the common techniques of the CRISPR-Cas9 system applied to virological studies and discuss the major findings using this system for studying enteric virus infection.
The Interactive Factors Contributing to Fear of Death

Despite the importance of the topic of death, a limited comprehensive statistical analysis conducted highlighting the complex association between fear of death and various variables. Thus, this study is conducted to account for the possible complexity by considering all interaction terms after reducing the dimensionality of a dataset by means of recursive feature elimination, followed by the removal of the multi-collinear variables. The results highlighted, for instance, although being married, older and female offset the negative associations of fear of death, their impacts are multiplicative. Also, those who think cryonics is desirable are associated with higher fear of death. For instance, while belief in cryonics is positively associated with fear of death, its association varies depending on the trouble that individuals experience that someday they would not be alive and their marital status.
Automated High-Definition MRI Processing Routine Robustly Detects Longitudinal Morphometry Changes in Alzheimer’s Disease Patients

Longitudinal MRI studies are of increasing importance to document the time course of neurodegenerative diseases as well as neuroprotective effects of a drug candidate in clinical trials. However, manual longitudinal image assessments are time consuming and conventional assessment routines often deliver unsatisfying study outcomes. Here, we propose a profound analysis pipeline that consists of the following coordinated steps: (1) an automated and highly precise image processing stream including voxel and surface based morphometry using latest highly detailed brain atlases such as the HCP MMP 1.0 atlas with 360 cortical ROIs; (2) a profound statistical assessment using a multiplicative model of annual percent change (APC); and (3) a multiple testing correction adopted from genome-wide association studies that is optimally suited for longitudinal neuroimaging studies. We tested this analysis pipeline with 25 Alzheimer’s disease patients against 25 age-matched cognitively normal subjects with a baseline and a 1-year follow-up conventional MRI scan from the ADNI-3 study. Even in this small cohort, we were able to report 22 significant measurements after multiple testing correction from SBM (including cortical volume, area and thickness) complementing only three statistically significant volume changes (left/right hippocampus and left amygdala) found by VBM. A 1-year decrease in brain morphometry coincided with an increasing clinical disability and cognitive decline in patients measured by MMSE, CDR GLOBAL, FAQ TOTAL and NPI TOTAL scores. This work shows that highly precise image assessments, APC computation and an adequate multiple testing correction can produce a significant study outcome even for small study sizes. With this, automated MRI processing is now available and reliable for routine use and clinical trials.
Ornithine α-Ketoglutarate Alleviates Inflammation via Regulating Ileal Mucosa Microbiota and Metabolites in Enterotoxigenic Escherichia coli-Infected Pigs

Enterotoxigenic Escherichia coli (ETEC) is one of the main causes of diarrhea in weaned piglets, and ornithine α-ketoglutarate (OKG) as a food supplement has been shown to improve intestinal immune status in animals and humans. However, it remains unknown whether OKG alleviates inflammation through the regulation of gut microbiota and its metabolites on ETEC-infected piglets. This study was conducted to explore the impact of OKG on growth performance, immunity, and ileal mucosa microbiota and its metabolites in piglets infected with ETEC. On a total of 40 pigs, a 2 × 2 factor design was performed; the major factors were diet (basal diet or 1% OKG diet) and challenge (E. coli or LB Broth). The results showed that ETEC-infection inhibited growth performance, and OKG supplementation alleviated growth performance. Interestingly, ETEC-infection increased the serum TNF-α and IL-6, decreased the serum IL-10, downregulated the mRNA expression of IL-1β, IL-6, MyD88, and improved the mRNA expression of IL-8, IL-18, and TLR4. OKG inhibited serum IL-6, suppressed the phosphorylation of downstream signals of NF-κB/JNK in the ileum, and enhanced serum IL-10 and ileum SIgA in ETEC-challenged piglets. OKG supplementation enhanced the mRNA expression of IL-1β and IL-10 and reduced NF-κB and MyD88 in the ileum. Importantly, OKG reversed intestinal microbiota dysfunction, including the diversity of ileal microbiota, the relative abundances of Actinobacillus, Turicibacter, and [Acetivibrio]_ethanolgignens_group, which significantly affected arachidonic acid metabolism and primary bile acid biosynthesis. Collectively, our results suggest that OKG improves growth performance, regulates immunity, and ileal mucosa microbiota and its metabolites in ETEC-infected piglets.
Transcriptomics and Network Pharmacology Reveal the Protective Effect of Chaiqin Chengqi Decoction on Obesity-Related Alcohol-Induced Acute Pancreatitis via Oxidative Stress and PI3K/Akt Signaling Pathway

Obesity-related acute pancreatitis (AP) is characterized by increasing prevalence worldwide and worse clinical outcomes compared to AP of other etiologies. Chaiqin chengqi decoction (CQCQD), a Chinese herbal formula, has long been used for the clinical management of AP but its therapeutic actions and the underlying mechanisms have not been fully elucidated. This study has investigated the pharmacological mechanisms of CQCQD in a novel mouse model of obesity-related alcohol-induced AP (OA-AP). The mouse OA-AP model was induced by a high-fat diet for 12 weeks and subsequently two intraperitoneal injections of ethanol, CQCQD was administered 2 h after the first injection of ethanol. The severity of OA-AP was assessed and correlated with changes in transcriptomic profiles and network pharmacology in the pancreatic and adipose tissues, and further docking analysis modeled the interactions between compounds of CQCQD and their key targets. The results showed that CQCQD significantly reduced pancreatic necrosis, alleviated systemic inflammation, and decreased the parameters associated with multi-organ dysfunction. Transcriptomics and network pharmacology analysis, as well as further experimental validation, have shown that CQCQD induced Nrf2/HO-1 antioxidant protein response and decreased Akt phosphorylation in the pancreatic and adipose tissues. In vitro, CQCQD protected freshly isolated pancreatic acinar cells from H2O2-elicited oxidative stress and necrotic cell death. The docking results of AKT1 and the active compounds related to AKT1 in CQCQD showed high binding affinity. In conclusion, CQCQD ameliorates the severity of OA-AP by activating of the antioxidant protein response and down-regulating of the PI3K/Akt signaling pathway in the pancreas and visceral adipose tissue.
Correlation Between Immune-Related Genes and Tumor-Infiltrating Immune Cells With the Efficacy of Neoadjuvant Chemotherapy for Breast Cancer

Background: In the absence of targeted therapy or clear clinically relevant biomarkers, neoadjuvant chemotherapy (NAC) is still the standard neoadjuvant systemic therapy for breast cancer. Among the many biomarkers predicting the efficacy of NAC, immune-related biomarkers, such as immune-related genes and tumor-infiltrating lymphocytes (TILs), play a key role. Methods: We analyzed gene expression from several datasets in the Gene Expression Omnibus (GEO) database and evaluated the relative proportion of immune cells using the CIBERSORT method. In addition, mIHC/IF detection was performed on clinical surgical specimens of triple-negative breast cancer patients after NAC. Results: We obtained seven immune-related genes, namely, CXCL1, CXCL9, CXCL10, CXCL11, IDO1, IFNG, and ORM1 with higher expression in the pathological complete response (pCR) group than in the non-pCR group. In the pCR group, the levels of M1 and γδT macrophages were higher, while those of the M2 macrophages and mast cells were lower. After NAC, the proportions of M1, γδT cells, and resting CD4 memory T cells were increased, while the proportions of natural killer cells and dendritic cells were decreased with downregulated immune-related genes. The results of mIHC/IF detection and the prognostic information of corresponding clinical surgical specimens showed the correlation of proportions of natural killer cells, CD8-positive T cells, and macrophages with different disease-free survival outcomes. Conclusion: The immune-related genes and immune cells of different subtypes in the tumor microenvironment are correlated with the response to NAC in breast cancer, and the interaction between TILs and NAC highlights the significance of combining NAC with immunotherapy to achieve better clinical benefits.