Miracle-dz/UniFAR-FTUs huggingface dataset:
A new way to estimate the age of bowhead whales (Balaena mysticetus) using ovarian corpora counts

We used lengths and reproductive data for bowhead whales (Balaena mysticetus L., 1758) harvested by Alaskan Eskimos to estimate female reproductive parameters and age. Data from 117 females determined that 75 were sexually mature and 42 were immature. Estimated length at sexual maturity was 13.35 m. Counts of ovarian corpora were obtained from 50 mature females. Corpora and baleen data were used with aspartic acid racemization (AAR) data to obtain estimated age at sexual maturity (ASM) at ≈26 years. The number of corpora counted in both ovaries (or estimated when only one ovary was counted) was used with ASM and estimated ovulation rate (OR) to obtain corpora age estimates ranging from 26 to 149 years. A stone harpoon tip recovered from whale 92B2 was consistent with her corpora age of 133 years. The correlation between corpora and AAR age estimates was 0.77. Estimated standard errors of corpora ages tended to be somewhat higher than those for comparable AAR ages. A sample of potentially mature females ex.
Reduction of pericardial effusion in advanced non-small cell lung cancer patients with KRAS, TP53, and MET mutation treated with nivolumab

Nivolumab is an immune checkpoint inhibitor that is used to treat various advanced cancers, including metastatic non-small cell lung cancer (NSCLC). Nivolumab treatment has different side effects. For this patient with advanced NSCLC, pericardial effusion was considered to be an immune-related adverse event after immunotherapy. It was characterized by deterioration of symptoms and considered to be pseudo-progression. The pericardial effusion gradually disappeared as nivolumab treatment continued during intensive follow-up monitoring. After chemotherapy and disease progression, the patient was treated with oral targeted therapy based on genes that were detected. After the re-imaging to assess the targeted therapy progress, immunotherapy was used. During immunotherapy, the patient showed increased pericardial effusion, and he underwent one pericardial puncture, in which 200 mL of pericardial effusion was drained. The pericardial effusion after puncture was not diagnosed as malignant by pathology, and the pericardial effusion remained. Shortness of breath continually improved during immunotherapy, and immunotherapy was continued with close observation. After 11 cycles, pericardial effusion had resolved. This case suggested that NSCLC pericardial effusion that was caused by an immune-related adverse event after immunotherapy might be considered to be pseudo-progression.
The Potential of Phytochemicals in Oral Cancer Prevention and Therapy: A Review of the Evidence

The etiological factors of oral cancer are complex including drinking alcohol, smoking tobacco, betel quid chewing, human papillomavirus infection, and nutritional deficiencies. Understanding the molecular mechanism of oral cancer is vital. The traditional treatment for patients with oral squamous cell carcinoma (e.g., surgery, radiotherapy, and chemotherapy) and targeted molecular therapy still have numerous shortcomings. In recent years, the use of phytochemical factors to prevent or treat cancer has received increasing attention. These phytochemicals have little or no toxicity against healthy tissues and are thus ideal chemopreventive agents. However, phytochemicals usually have low water solubility, low bioavailability, and insufficient targeting which limit therapeutic use. Numerous studies have investigated the development of phytochemical delivery systems to address these problems. The present article provides an overview of oral cancer including the etiological factors, diagnosis, and traditional therapy. Furthermore, the classification, dietary sources, anticancer bioactivity, delivery system improvements, and molecular mechanisms against oral cancer of phytochemicals are also discussed in this review.
Nanoporous Anodic Aluminum-Iron Oxide with a Tunable Band Gap Formed on the FeAl3 Intermetallic Phase

Nanostructured anodic oxide layers on an FeAl3 intermetallic alloy was prepared by two-step anodization in 20 wt. % H2SO4 at 0 °C. The obtained anodic oxide coating was subjected to phase and chemical composition analysis using XPS and XRD techniques. An analysis of the band gap of individual coatings was also performed. The applied parameters of the anodization process were determined, enabling the formation of a nanostructured coating on the FeAl3 intermetallic alloy. Tests were carried out on samples produced at a voltage between 10 V and 22.5 V in 2.5 V steps. The produced coatings were subjected to an annealing process at 900 °C for 2 h in an argon protective atmosphere. Moreover, the influence of the substrate chemical composition on the chemical and phase composition of the anodic oxide are discussed. Band gaps of 2.37 eV at 22.5 V and 2.64 eV at 10 V were obtained directly after the anodizing process. After applying the heat treatment, band gap values of 2.10 eV at 22.5 Vand 2.48 eV for the coating produced at 10 V were obtained.
Use of somatic cell count as an indicator of colostrum quality

The impact of cow mammary gland diseases on the quality of colostrum is not conclusively defined; research results are conflicting. However, it is widely believed that mastitis lowers the level of immunoglobulins and the quality of the colostrum produced. Therefore, the aim of this study was to determine the influence of somatic cell counts (SCC) on the colostrum immunostimulating and chemical components. The experiment was conducted on an experimental organic dairy farm in which a herd of approximately 250 cows was kept in a freestall housing system, with the average performance exceeding 6,000 kg of milk per lactation. Colostrum and milk samples were taken individually from each cow seven times during the experiment: from the first to second day after calving–twice per day, and from the third to fifth day after calving–once per day. Therefore, after preliminary analyses, the cows were divided into two groups based on the cytological quality of their colostrum at the first collection: 1. SCC ≤400,000 cells/ml (good quality colostrum; GCC– 18 cows), 2. SCC ≥ 400,000 cells/ml (low quality colostrum; LCC– 22 cows). The study found almost double the concentration of immunoglobulins and essential fatty acids in first milking colostrum in the GCC group than in colostrum from the LCC group. In addition, an increase in the concentration of lysozyme in first milking colostrum was associated with a decrease in the concentration of immunoglobulins. In addition, the increase in the level of lysozyme was associated with a decrease in the concentration of immunoglobulins. In conclusion, the SCC of first milking colostrum can be used as an indicator of colostrum quality.
Experimental Pretreatment with Chlorogenic Acid Prevents Transient Ischemia-Induced Cognitive Decline and Neuronal Damage in the Hippocampus through Anti-Oxidative and Anti-Inflammatory Effects

Chlorogenic acid (CGA), an ester of caffeic acid and quinic acid, is among the phenolic acid compounds which can be naturally found in green coffee extract and tea. CGA has been studied since it displays significant pharmacological properties. The aim of this study was to investigate the effects of CGA on cognitive function and neuroprotection including its mechanisms in the hippocampus following transient forebrain ischemia in gerbils. Memory and learning following the ischemia was investigated by eight-arm radial maze and passive avoidance tests. Neuroprotection was examined by immunohistochemistry for neuronal nuclei-specific protein and Fluoro-Jade B histofluorescence staining. For mechanisms of the neuroprotection, alterations in copper, zinc-superoxide dismutase (SOD1), SOD2 as antioxidant enzymes, dihydroethidium and 4-hydroxy-2-nonenal as indicators for oxidative stress, and anti-inflammatory cytokines (interleukin (IL)-4 and IL-13) and pro-inflammatory cytokines (tumor necrosis factor α (TNF-α) and IL-2) were examined by Western blotting and/or immunohistochemistry. As a result, pretreatment with 30 mg/kg CGA attenuated cognitive impairment and displayed a neuroprotective effect against transient forebrain ischemia (TFI). In Western blotting, the expression levels of SOD2 and IL-4 were increased due to pretreatment with CGA and, furthermore, 4-HNE production and IL-4 expressions were inhibited by CGA pretreatment. Additionally, pretreated CGA enhanced antioxidant enzymes and anti-inflammatory cytokines and, in contrast, attenuated oxidative stress and pro-inflammatory cytokine expression. Based on these results, we suggest that CGA can be a useful neuroprotective material against ischemia-reperfusion injury due to its antioxidant and anti-inflammatory efficacies.
Mycoplasma bovis Infections—Occurrence, Diagnosis and Control

Mycoplasma bovis is a cause of bronchopneumonia, mastitis and arthritis but may also affect other main organs in cattle such us the eye, ear or brain. Despite its non-zoonotic character, M. bovis infections are responsible for substantial economic health and welfare problems worldwide. M. bovis has spread worldwide, including to countries for a long time considered free of the pathogen. Control of M. bovis infections is hampered by a lack of effective vaccines and treatments due to increasing trends in antimicrobial resistance. This review summarizes the latest data on the epizootic situation of M. bovis infections and new sources/routes of transmission of the infection, and discusses the progress in diagnostics. The review includes various recommendations and suggestions which could be applied to infection control programs.
Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation

Simple Summary The Pura Raza Español horse (PRE) is an autochthonous Spanish horse recognized as an official breed since the 15th century. In 1912, with the creation of its studbook, it became a closed population (only animals belonging to the breed acts as breeders: 23,530 stallions and 75,870 mares), in which relatedness between individuals and inbreeding has tended to increase. Inbreeding estimation measures the probability in an individual of possessing, in one gene, two identical alleles derived from a common ancestor. Each common ancestor provides part of the descendant’s total inbreeding (partial inbreeding coefficient, Fij). This work analyzes the Fij, calculated using a recently developed approach (based on founders and Mendelian sampling of the non-founders) in the whole PRE population. The identification of 10,244 common ancestors and their relationship with the seven most influential individuals of the breed allowed us to determine that a genetic bottleneck due to an unequal contribution over the generations occurred. Computing Fij has being an important tool to determine which are the breeding animals, with more or less massive use, whose are determining a loss of genetic variability in the population at each moment and has enabled us to expand our knowledge about PRE genetic demographic evolution. Abstract The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of Fij by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals’ breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.
What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?

Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
Effect of feeding diets high in monounsaturated fatty acids and α-tocopheryl acetate to rabbits on resulting carcass fatty acid profile and lipid oxidation

The effects of olive (MONO) or sunflower (POLY) oil-enriched (30 g/kg) diets with either a basal (10 mg/kg food) or supplemented (200 mg/kg) level of a-tocopheryl acetate on some measures of production, fatty acid composition of animal tissues and susceptibility to oxidation of rabbit meat and membrane extracts have been studied. MONO diet produced higher levels of C18:1 in animal tissues. Animals that received POLY diet had a higher level of C18:2 in perirenal and neutral fraction of intramuscular fat and higher levels of C18:2, C20:4, C22:4 and C22:5 in phospholipid, reaching a higher overall unsaturation (P = 0·001). Muscle samples from rabbits given the POLY diet were more susceptible to lipid oxidation (P = 0·0001). Differences in membrane lipid oxidation, between groups followed a similar pattern to that of meat. Diets rich in C18:2 resulted in increases in concentration of pentanal (P
Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS

Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.
Induction of CD4+CD25+ Regulatory T Cells from In Vitro Grown Human Mononuclear Cells by Sparteine Sulfate and Harpagoside

Regulatory T cells (Tregs) are key players in the regulation of inflammatory responses. In this study, two natural molecules, namely, sparteine sulfate (SS) and harpagoside (Harp), were investigated for their ability to induce Tregs in human peripheral blood mononuclear cells (PBMCs). PBMCs were isolated from healthy volunteers and grown in the presence or absence of ConA, with TGF-beta, SS or Harp. Expression of the mRNA of FoxP3, TGF-beta, IL-10 and GAPDH was assessed via q-PCR. The expression of Treg markers including CD4, CD25, CD127 and FoxP3 was measured via flow cytometry. The secretion of IL-10 and TGF-beta by cultured cells was assessed by ELISA. Furthermore, the suppressive role of SS and Harp on PBMCs in vitro was tested via allogeneic mixed lymphocyte reaction (MLR). Data obtained show that both compounds increased the expression of FoxP3, TGF-beta and IL-10 mRNA in resting PBMCs but to a lesser extent in activated cells. Moreover, they significantly increased the percent of CD4+CD25+FoxP3+CD127− Tregs in activated and naïve PBMCs. Functionally, both compounds caused a significant reduction in the stimulation index in allogeneic MLR. Together, our data demonstrate for the first time that SS and Harp can induce human Tregs in vitro and therefore have great potential as anti-inflammatory agents.
The Significance of Color Change in Newly Metamorphosed American Toads (Bufo a. americanus)

Color change in newly metamorphosed toards was analyzed as a funciton of background color, temperature, and desiccation. Toads showed no tendency to change color as a function of desiccation or temperature. Toads kept on light or dark substrates could darken or lighten (measured by comparison to Munsell Soil Color Charts), respectively, an average of 2 Munsell Color Values over a 2 h period. About half of the color change occurred within the first 15 min, and the rate of color change was low after onehalf hour. Actively-hunting garter snakes caught more dark-matched than light-matched toads on a lightcolored background (sand), but there was no difference in capture rates between dark- and light-matched toads on a dark-colored background (top soil). Both dark- and light-matched toads preferred the dark background, and toads moved less frequently on the dark background
Feature Selection for Health Care Costs Prediction Using Weighted Evidential Regression †

Although many authors have highlighted the importance of predicting people’s health costs to improve healthcare budget management, most of them do not address the frequent need to know the reasons behind this prediction, i.e., knowing the factors that influence this prediction. This knowledge allows avoiding arbitrariness or people’s discrimination. However, many times the black box methods (that is, those that do not allow this analysis, e.g., methods based on deep learning techniques) are more accurate than those that allow an interpretation of the results. For this reason, in this work, we intend to develop a method that can achieve similar returns as those obtained with black box methods for the problem of predicting health costs, but at the same time it allows the interpretation of the results. This interpretable regression method is based on the Dempster-Shafer theory using Evidential Regression (EVREG) and a discount function based on the contribution of each dimension. The method “learns” the optimal weights for each feature using a gradient descent technique. The method also uses the nearest k-neighbor algorithm to accelerate calculations. It is possible to select the most relevant features for predicting a patient’s health care costs using this approach and the transparency of the Evidential Regression model. We can obtain a reason for a prediction with a k-NN approach. We used the Japanese health records at Tsuyama Chuo Hospital to test our method, which included medical examinations, test results, and billing information from 2013 to 2018. We compared our model to methods based on an Artificial Neural Network, Gradient Boosting, Regression Tree and Weighted k-Nearest Neighbors. Our results showed that our transparent model performed like the Artificial Neural Network and Gradient Boosting with an R2 of 0.44.
Novel Methodologies for Chemical Activation in Organic Synthesis under Solvent-Free Reaction Conditions

One central challenge for XXI century chemists is the development of sustainable processes that do not represent a risk either to humanity or to the environment. In this regard, the search for more efficient and clean alternatives to achieve the chemical activation of molecules involved in chemical transformations has played a prominent role in recent years. The use of microwave or UV-Vis light irradiation, and mechanochemical activation is already widespread in many laboratories. Nevertheless, an additional condition to achieve “green” processes comes from the point of view of so-called atom economy. The removal of solvents from chemical reactions generally leads to cleaner, more efficient and more economical processes. This review presents several illustrative applications of the use of sustainable protocols in the synthesis of organic compounds under solvent-free reaction conditions.
CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis

SUMMARY CONAN is a web application developed to detect specificity determinants and function related sites by amino acids co-variation networks analysis, emphasizing local co-evolutionary constraints. The software allows the characterization of structurally and functionally relevant groups of residues and their relationship with subsets of sequences by automatic cross-referencing with GO terms, UniprotKb annotations and INTERPRO. AVAILABILITY CONAN is free and open-source, being distributed in the terms of the GPLV3 licence. The software is available as a web application and python script versions and can be accessed at http://bioinfo.icb. ufmg.br/conan. We also provide running instructions, the source code and a user guide.