Miracle-dz/UniFAR-FTUs huggingface dataset:
Feeding Strategies to Reduce Nutrient Losses and Improve the Sustainability of Growing Pigs

The efficiency of pig production using nutrients has increased over the years. Still, better efficiency of nutrient utilization can be achieved by feeding pigs with diets adjusted to their estimated requirements. An increase in nutrient efficiency of utilization represents economic gains while maximizing environmental performance. The objective of this paper is to review the impact of different methods of diet formulation that provide farm animals with the amount of nutrients to satisfy their needs while minimizing nutrient excretion and greenhouse gas emissions. Diet formulation is one tool that can help to maximize nitrogen and energy utilization by decreasing crude protein content in diets. The use of local feedstuff and non-human-edible products (e.g., canola meal) associated with synthetic amino acid inclusion in the diet are valuable techniques to reduce carbon footprint. Precision feeding and nutrition is another powerful tool that allows not only daily tailoring of diets for maximal nutrient efficiency of utilization but also to reduce costs and improve nitrogen efficiency of utilization. In this review, we simulated through mathematical models the nitrogen and energy efficiency of utilization resulting from crude protein reduction in the diet. An 8% crude protein reduction in the diet can increase nitrogen efficiency of utilization by 54% while costing 11% less than a control diet without synthetic amino acids. The same reduction in crude protein represented a major improvement in available energy due to the decrease of energetic losses linked to protein deamination. Urinary and hindgut fermentation energy losses were 24% lower for pigs fed with low-protein diets when compared to control diets. In terms of modern feeding techniques and strategies, precision feeding and nutrition can decrease nitrogen excretion by 30% when compared to group phase feeding. The benefits of feeding pigs with low-protein diets and precision feeding techniques are additive and might result in a 61% nitrogen efficiency of utilization. There is room for improvement in the way nutrient requirements are estimated in pigs. Improving the understanding of the variation of nutrient utilization among pigs can contribute to further environmental gains.
Efficacy and Safety of PARP Inhibitors in Advanced or Metastatic Triple-Negative Breast Cancer: A Systematic Review and Meta-Analysis

Purpose Poly (ADP-ribose) polymerase (PARP) inhibitors have shown promising results in metastatic triple-negative breast cancers (TNBCs). We therefore performed a systematic review and meta-analysis to evaluate the efficacy and safety of this drug in patients with advanced or metastatic TNBC. Methods A systematic literature search of PubMed, Embase, Scopus, Web of Science, and Cochrane Central Register of Controlled Trials for synonyms of “PARP inhibitors” and “breast cancer” was carried out. All published phase II/III clinical studies of PARP inhibitors in patients with advanced/metastatic TNBC were screened. Data were extracted independently by two authors and analyzed using Review Manager software version 5.3. End points include overall response rate (ORR), progression-free survival (PFS), and adverse events. Results Ten clinical trials were identified, with a total of 1,495 patients included. Pooled analyses showed that PARP inhibitors could provide a significant improvement of ORR [risk ratio (RR) = 2.00; 95% confidence interval (CI), 1.14–3.50; p = 0.02) and PFS [hazard ratio (HR) = 0.68; 95%Cl, 0.59–0.77; p < 0.0001) compared to chemotherapy in the whole population. In subgroup analysis, patients with BRCA mutation had a higher objective response to PARP inhibitor, with an RR of 2.85 (95%CI, 1.34–6.06; p = 0.007) compared to BRCA wild-type patients. However, no significant difference in ORR was observed between the homologous recombination deficiency (HRD) positive and non-HRD subgroups (RR = 1.82; 95%CI, 0.81–4.08; p = 0.14). Hematological toxicity is a common adverse event of PARP inhibitors. Conclusions PARP inhibitors are effective options for the treatment of patients with advanced or metastatic TNBC. Compared with patients without germline BRCA mutation, patients with germline BRCA mutation could benefit more from PARP inhibitors. In clinical setting, hematological toxicity associated with PARP inhibitors should be monitored regularly.
Evaluation of a Sexual Transmitted Infection Prevention Program Among University Students in Beira City Central Mozambique: A Study Protocol

Background: Unhealthy sexual behaviors, such as unprotected sexual intercourse and lack of using screening services increase cyclical transmission of sexually transmitted infections including Human Immunodeficiency Virus (HIV), especially among young adults. Hence health promotion programs can contribute to reduce the consequences, by changing (determinants of) these behaviors. Such interventions need to embrace a comprehensive approach and apply theory-and evidence-based methods. This article describes the protocol for a process and effect evaluation study of a sexually transmitted infection prevention program among university students in Beira city, central Mozambique. Methods: The on-going program at Universidade Católica de Moçambique is described following the six steps of Intervention Mapping (IM), with a focus on the evaluation plan (i.e., the final step in IM). The details regarding previous steps in the protocol are briefly described as well, as they lay the foundation for the final step. The overall study will apply a hybrid type 1 approach by assessing the effectiveness of the intervention while gettering implementation. The process evaluation will apply qualitative and quantitative methods to gain insight in the context, reach, dose delivered, dose received and recruitment. Interviews with closed and open-ended questions will be conducted with program implementers and users. A quasi-experimental non-equivalent control group design is used to evaluate the effectiveness. A cohort of university students will be followed for 6 months. Self-administrated questionnaires will be used to collect data every 3 months. Discussion: A combination of process and effect evaluation is proposed. This is a useful and fruitful procedure, since concurrent process evaluation can allow researchers to better interpret findings from the effect evaluation and understand how the intervention might replicate in similar contexts. We decided to follow the IM approach since, it is a theory-and evidence-based, systematic and detailed guide regarding what to do at every steps. A quasi-experimental non-equivalent control group design was chosen to fit the context of the study and generate outcomes with high external validity. Study Registration: 004/CIBS/2020.
Mood Disturbances, Anxiety, and Impact on Quality of Life in Patients Admitted to Epilepsy Monitoring Units

Introduction: The overall combined prevalence of anxiety and depression in patients with epilepsy has been estimated at 20.2 and 22.9%, respectively, and is considered more severe in drug-refractory epilepsy. Patients admitted to epilepsy monitoring units constitute a particular group. Also, patients with psychogenic non-epileptic seizures can reach more than 20% of all admissions. This study aims to characterize these symptoms in a large cohort of patients admitted for evaluation in a tertiary epilepsy center. Materials and Methods: The study was conducted among 493 consecutive patients (age: 38.78 ± 12.7, 57% females) admitted for long-term video EEG from January 2013 to February 2021. Demographic, clinical, and mood disorder patients' data were collected. Anxiety and depression symptoms were assessed through the Hospital Anxiety Depression Scale (HADS-A and HADS-D), the State Trait Anxiety Inventory (STAI), and Beck Depression Inventory (BDI-II). Quality of life was determined using the QOLIE-10. Patients were divided into three groups: patients with epilepsy (n = 395), psychogenic non-epileptic seizures (PNES) (n = 56), and combined (n = 33). A univariate and multivariate regression analysis was performed for variables associated with quality of life. Results: Of 493 patients, 45.0% had structural etiology, and considering epilepsy classification, 43.6% were of temporal lobe origin. In addition, 32.45% of patients had a previous psychiatric history, 49.9% of patients had depressive symptoms in BDI, and 30.9% according to HADS-D; 56.42 and 52.63% of patients presented pathological anxiety scores in STAI-T and STAI-S, respectively; and 44.78% according to HADS-A. PNES and combined groups revealed a higher incidence of pathologic BDI scores (64.29 and 78.79%, p < 0.001) as well as pathologic HADS-A scores (p = 0.001). Anxiety and depression pathologic results are more prevalent in females, HADS-A (females = 50.7%, males = 36.8%; p = 0.0027) and BDI > 13 (females = 56.6%, males = 41.0%; p = 0.0006). QOLIE-10 showed that 71% of the patients had their quality of life affected with significantly higher scores in the combined group than in the epilepsy and PNES groups (p = 0.0015). Conclusions: Subjective anxiety, depression, and reduced quality of life are highly prevalent in patients with refractory epilepsy. These symptoms are more evident when PNES are associated with epilepsy and more severe among female patients. Most of the cases were not previously diagnosed. These factors should be considered in everyday clinical practice, and specific approaches might be adapted depending on the patient's profile.
Effects of Sex, Age, and Apolipoprotein E Genotype on Brain Ceramides and Sphingosine-1-Phosphate in Alzheimer’s Disease and Control Mice

Apolipoprotein ε4 (APOE)4 is a strong risk factor for the development of Alzheimer’s disease (AD) and aberrant sphingolipid levels have been implicated in AD. We tested the hypothesis that the APOE4 genotype affects brain sphingolipid levels in AD. Seven ceramides and sphingosine-1-phosphate (S1P) were quantified by LC-MSMS in hippocampus, cortex, cerebellum, and plasma of <3 months and >5 months old human APOE3 and APOE4-targeted replacement mice with or without the familial AD (FAD) background of both sexes (145 animals). APOE4 mice had higher Cer(d18:1/24:0) levels in the cortex (1.7-fold, p = 0.002) than APOE3 mice. Mice with AD background showed higher levels of Cer(d18:1/24:1) in the cortex than mice without (1.4-fold, p = 0.003). S1P levels were higher in all three brain regions of older mice than of young mice (1.7-1.8-fold, all p ≤ 0.001). In female mice, S1P levels in hippocampus (r = −0.54 [−0.70, −0.35], p < 0.001) and in cortex correlated with those in plasma (r = −0.53 [−0.71, −0.32], p < 0.001). Ceramide levels were lower in the hippocampus (3.7–10.7-fold, all p < 0.001), but higher in the cortex (2.3–12.8-fold, p < 0.001) of female than male mice. In cerebellum and plasma, sex effects on individual ceramides depended on acyl chain length (9.5-fold lower to 11.5-fold higher, p ≤ 0.001). In conclusion, sex is a stronger determinant of brain ceramide levels in mice than APOE genotype, AD background, or age. Whether these differences impact AD neuropathology in men and women remains to be investigated.
Observation of the Gut Microbiota Profile in C57BL/6 Mice Induced by Plasmodium berghei ANKA Infection

The genus of Plasmodium parasites can cause malaria, which is a prevalent infectious disease worldwide, especially in tropical and subtropical regions. C57BL/6 mice infected with P. berghei ANKA (PbA) will suffer from experimental cerebral malaria (ECM). However, the gut microbiota in C57BL/6 mice has rarely been investigated, especially regarding changes in the intestinal environment caused by infectious parasites. P. berghei ANKA-infected (PbA group) and uninfected C57BL/6 (Ctrl group) mice were used in this study. C57BL/6 mice were infected with PbA via intraperitoneal injection of 1 × 106 infected red blood cells. Fecal samples of two groups were collected. The microbiota of feces obtained from both uninfected and infected mice was characterized by targeting the V4 region of the 16S rRNA through the Illumina MiSeq platform. The variations in the total gut microbiota composition were determined based on alpha and beta diversity analyses of 16S rRNA sequencing. The raw sequences from all samples were generated and clustered using ≥ 97% sequence identity into many microbial operational taxonomic units (OTUs). The typical microbiota composition in the gut was dominated by Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia at the phylum level. Bacteroidetes and Verrucomicrobia were considerably decreased after PbA infection compared with the control group (Ctrl), while Firmicutes and Proteobacteria were increased substantially after PbA infection compared with Ctrl. The alpha diversity index showed that the observed OTU number was increased in the PbA group compared with the Ctrl group. Moreover, the discreteness of the beta diversity revealed that the PbA group samples had a higher number of OTUs than the Ctrl group. LEfSe analysis revealed that several potential bacterial biomarkers were clearly related to the PbA-infected mice at the phylogenetic level. Several bacterial genera, such as Acinetobacter, Lactobacillus, and Lachnospiraceae_NK4A136_group, were overrepresented in the PbA-infected fecal microbiota. Meanwhile, a method similar to gene coexpression network construction was used to generate the OTU co-abundance units. These results indicated that P. berghei ANKA infection could alter the gut microbiota composition of C57BL/6 mice. In addition, potential biomarkers should offer insight into malaria pathogenesis and antimalarial drug and malaria vaccine studies.
Lipid Peroxide-Derived Reactive Carbonyl Species as Mediators of Oxidative Stress and Signaling

Oxidation of membrane lipids by reactive oxygen species (ROS) or O2/lipoxygenase leads to the formation of various bioactive compounds collectively called oxylipins. Reactive carbonyl species (RCS) are a group of oxylipins that have the α,β-unsaturated carbonyl structure, including acrolein and 4-hydroxy-(E)-2-nonenal. RCS provides a missing link between ROS stimuli and cellular responses in plants via their electrophilic modification of proteins. The physiological significance of RCS in plants has been established based on the observations that the RCS-scavenging enzymes that are overexpressed in plants or the RCS-scavenging chemicals added to plants suppress the plants’ responses to ROS, i.e., photoinhibition, aluminum-induced root damage, programmed cell death (PCD), senescence, abscisic acid-induced stomata closure, and auxin-induced lateral root formation. The functions of RCS are thus a key to ROS- and redox-signaling in plants. The chemical species involved in distinct RCS signaling/damaging phenomena were recently revealed, based on comprehensive carbonyl determinations. This review presents an overview of the current status of research regarding RCS signaling functions in plants and discusses present challenges for gaining a more complete understanding of the signaling mechanisms.
Single-cell RNA Sequencing Reveals Heterogeneity of Cultured Bovine Satellite Cells

Skeletal muscle from meat-producing livestock such as cattle is a major source of food for humans. To improve skeletal muscle growth efficiency or quality in cattle, it is necessary to understand the genetic and physiological mechanisms that govern skeletal muscle composition, development, and growth. Satellite cells are the myogenic progenitor cells in postnatal skeletal muscle. In this study we analyzed the composition of bovine satellite cells with single-cell RNA sequencing (scRNA-seq). We isolated satellite cells from a 2-week-old male calf, cultured them in growth medium for a week, and performed scRNA-seq using the 10x Genomics platform. Deep sequencing of two scRNA-seq libraries constructed from cultured bovine satellite cells yielded 860 million reads. Cell calling analyses revealed that these reads were sequenced from 19,096 individual cells. Clustering analyses indicated that these reads represented 15 cell clusters that differed in gene expression profile. Based on the enriched expression of markers of satellite cells (PAX7 and PAX3), markers of myoblasts (MYOD1, MYF5), and markers of differentiated myoblasts or myocytes (MYOG), three clusters were determined to be satellite cells, two clusters myoblasts, and two clusters myocytes. Gene ontology and trajectory inference analyses indicated that cells in these myogenic clusters differed in proliferation rate and differentiation stage. Two of the remaining clusters were enriched with PDGFRA, a marker of fibro-adipogenic (FAP) cells, the progenitor cells for intramuscular fat, and are therefore considered to be FAP cells. Gene ontology analyses indicated active lipogenesis in one of these two clusters. The identity of the remaining six clusters could not be defined. Overall, the results of this study support the hypothesis that bovine satellite cells are composed of subpopulations that differ in transcriptional and myogenic state. The results of this study also support the hypothesis that intramuscular fat in cattle originates from fibro-adipogenic cells.
Changes in Social, Romantic, and General Life Satisfaction Over the Course of a Substance Use Disorder

Background: The pandemic has highlighted the importance of social connection for health and well-being. Satisfaction across domains of life is associated with substance use outcomes, such as risk of relapse and mortality. Previous work has delineated the relationship between substance use and social connections, yet there is a lack of research exploring the relationship between substance use and satisfaction with domains of life over time. Methods: We retrospectively assessed satisfaction with social life, romantic life, and general life across five phases of substance use among 339 adults, of whom 289 identify as formerly having a problem with substance use, and a comparison group of 50 who report no history of problematic drug use. We compared those whose primary drug of choice was alcohol, marijuana, methamphetamine, non-prescription opioids, and prescription opioids. Results: Those who used prescription opioids reported a larger drop in satisfaction in social life, romantic life, and general life during the course of substance use than those who used other drugs. However, we report no significant differences in current satisfaction, social well-being, or quality of life between people in recovery and people with no history of problematic substance use. Conclusions: These findings—alongside neuropsychological work on the opioid system and sociality—paint a picture that those who formerly used prescription opioids may experience lower satisfaction across life domains during the course of their substance use than those who used other substances. However, people in prolonged recovery—regardless of their drug of choice—all show similar levels of satisfaction compared to people with no history of problematic substance use.
Non-invasive Biofouling Monitoring to Assess Drinking Water Distribution System Performance

Biofilms are endemic in drinking water distribution systems (DWDS), forming on all water and infrastructure interfaces. They can pose risks to water quality and hence consumers. Our understanding of these biofilms is limited, in a large part due to difficulties in sampling them without unacceptable disruption. A novel, non-destructive and non-disruptive biofilm monitoring device (BMD), which includes use of flow cytometry analysis, was developed to assess biofouling rates. Laboratory based experiments established optimal configurations and verified reliable cell enumeration. Deployment at three operational field sites validated assessment of different biofouling rates. These differences in fouling rates were not obvious from bulk water sampling and analysis, but did have a strong correlation with long-term performance data of the associated networks. The device offers the potential to assess DWDS performance in a few months, compared to the number of years required to infer findings from historical customer contact data. Such information is vital to improve the management of our vast, complex and uncertain drinking water supply systems; for example rapidly quantifying the benefits of improvements in water treatment works or changes to maintenance of the network.
Tumor Microenvironment Profiles Reveal Distinct Therapy-Oriented Proteogenomic Characteristics in Colorectal Cancer

Advances in immunotherapy have made an unprecedented leap in treating colorectal cancer (CRC). However, more effective therapeutic regimes need a deeper understanding of molecular architectures for precise patient stratification and therapeutic improvement. We profiled patients receiving neoadjuvant chemotherapy alone or in combination with immunotherapy (PD-1 checkpoint inhibitor) using Digital Spatial Profiler (DSP), a high-plex spatial proteogenomic technology. Compartmentalization-based high-plex profiling of both proteins and mRNAs revealed pronounced immune infiltration at tumor regions associated with immunotherapy treatment. The protein and the corresponding mRNA levels within the same selected regions of those patient samples correlate, indicating an overall concordance between the transcriptional and translational levels. An elevated expression of PD-L1 at both protein and the mRNA levels was discovered in the tumor compartment of immunotherapy-treated patients compared with chemo-treated patients, indicating potential prognostic biomarkers are explorable in a spatial manner at the local tumor microenvironment (TME). An elevated expression of PD-L1 was verified by immunohistochemistry. Other compartment-specific biomarkers were also differentially expressed between the tumor and stromal regions, indicating a dynamic interplay that can potentiate novel biomarker discovery from the TME perspectives. Simultaneously, a high-plex spatial profiling of protein and mRNA in the tumor microenvironment of colorectal cancer was performed.
Targeting Phosphatases and Kinases: How to Checkmate Cancer

Metastatic disease represents the major cause of death in oncologic patients worldwide. Accumulating evidence have highlighted the relevance of a small population of cancer cells, named cancer stem cells (CSCs), in the resistance to therapies, as well as cancer recurrence and metastasis. Standard anti-cancer treatments are not always conclusively curative, posing an urgent need to discover new targets for an effective therapy. Kinases and phosphatases are implicated in many cellular processes, such as proliferation, differentiation and oncogenic transformation. These proteins are crucial regulators of intracellular signaling pathways mediating multiple cellular activities. Therefore, alterations in kinases and phosphatases functionality is a hallmark of cancer. Notwithstanding the role of kinases and phosphatases in cancer has been widely investigated, their aberrant activation in the compartment of CSCs is nowadays being explored as new potential Achille’s heel to strike. Here, we provide a comprehensive overview of the major protein kinases and phosphatases pathways by which CSCs can evade normal physiological constraints on survival, growth, and invasion. Moreover, we discuss the potential of inhibitors of these proteins in counteracting CSCs expansion during cancer development and progression.