Miracle-dz/UniFAR-FTUs huggingface dataset:
Source‐sink populations in Mediterranean Blue tits: evidence using single‐locus minisatellite probes

Long term studies on population biology of Blue tits (Parus caeruleus L.) in Mediterranean habitats have shown that in patchy landscapes life‐history traits seem to be adapted to the predominant type of habitat, where reproductive success is higher. The “source‐sink hypothesis” suggests that differences in the local production of fledglings result in an asymmetrical gene flow from rich deciduous habitats (“source”) to evergreen poor habitats (“sink”), preventing local adaptation in evergreen habitats.
Methods for Establishment and Maintenance of Germ-Free Rat Models

Numerous studies have demonstrated that the gut microbiota plays a vital role in human health and disease development. Although the number of studies on host–microbiota interactions have increased in recent years, the underlying pathogenesis of dysbiosis-related diseases are still largely unknown. Germ-free (GF) rodent models, with the animals housed in sterile isolators and completely free of microbiota, are useful tools to advance our understanding of host–microbiota relationship in vivo. Although protocols concerning the establishment and maintenance of GF mouse models have previously been reported, the establishment, maintenance and monitoring of GF rodents are labor-intensive, tedious and take experience and skills. The aim of our study was to establish a GF rat model for the following microbiota-related researches and provide an easy-to-use protocol for the establishment and maintenance of GF rat model in detail, including steps to set up the isolator, sterilize the flexible isolator bubble, import food, water and other supplies, and methods to acquire newborn GF rats, hand rearing of suckling GF rats and reproduction of GF offspring. During the hand feeding period, the body weight of suckling GF rats was weighed once a day to ascertain the amount of artificial milk was given. Based on our results, the body weight of suckling GF rats decreased 1 week after birth and then began to increase. Methods for verifying the quality of the model like assessing the sterile status of the rat colony are also described. Moreover, possible difficulties and challenges, especially during gavage, and suggestions to avoid contamination will be discussed. The protocol presented will facilitate the establishment of GF rat models and downstream microbiota-related researches.
On-Sight and Red-Point Climbing: Changes in Performance and Route-Finding Ability in Male Advanced Climbers

Aim In lead climbing, the ascent of the route can be defined as on-sight or red-point. On-sight is the more challenging style since it demands greater physiological and psychological commitment. The differences between the two modes in advanced climbers have not been studied much. Two essential skills needed to optimize performance, in both on-sight and in red-point climbing, are route interpretation (RI) ability and movements sequence recall. Therefore, this study aimed to compare performance between on-sight and red-point ascent in advanced climbers and evaluate how a climber’s RI ability and movement sequences recall might change before and after on-sight and red-point climbing. Methods Eighteen advanced male climbers (age 29.2 ± 4.7 years, body mass 67.8 ± 3.6 kg, stature 175.2 ± 2.4 cm, best red-point and on-sight grades 7b+/8a and 7a+/7b+, respectively) were video-recorded during the route ascent in on-sight and red-point modes to evaluate performance and to measure static and dynamic action times. RI ability and movement sequence recall were assessed before and after each climb. Level of anxiety was evaluated via a self-report questionnaire. Heart rate (fH), lactate concentration, ([La–]), and rating of perceived exertion (RPE) were detected during and after each climb. Results Compared to on-sight, an improvement in performance was observed in a red-point climb: the ascent was faster (148.7 ± 13.6 s and 179.5 ± 12.5 s, respectively, P < 0.05), smoother (significant reduction in exploratory moves and in stops times, P < 0.05), less demanding physiologically (lower fHpeak and [La–]peak, P < 0.05), and psychologically (lower RPE, cognitive and somatic anxiety and higher self-confidence, P < 0.05). The RI ability was improved in red-point versus on-sight and, in the same mode, between pre and post ascent. Conclusion Red-point climbing was found to be less demanding than on-sight, both physiologically and psychologically, under the conditions investigated by this study. Our findings suggest that RI is a trainable skill and underscore the importance of including specific techniques in training programs designed to improve interaction between perceptual, psychological, and physiological factors.
Label-Free Infrared Spectral Histology of Skin Tissue Part II: Impact of a Lumican-Derived Peptide on Melanoma Growth

Melanoma is the most aggressive type of cutaneous malignancies. In addition to its role as a regulator of extracellular matrix (ECM) integrity, lumican, a small leucine-rich proteoglycan, also exhibits anti-tumor properties in melanoma. This work focuses on the use of infrared spectral imaging (IRSI) and histopathology (IRSH) to study the effect of lumican-derived peptide (L9Mc) on B16F1 melanoma primary tumor growth. Female C57BL/6 mice were injected with B16F1 cells treated with L9Mc (n = 10) or its scrambled peptide (n = 8), and without peptide (control, n = 9). The melanoma primary tumors were subjected to histological and IR imaging analysis. In addition, immunohistochemical staining was performed using anti-Ki-67 and anti-cleaved caspase-3 antibodies. The IR images were analyzed by common K-means clustering to obtain high-contrast IRSH that allowed identifying different ECM tissue regions from the epidermis to the tumor area, which correlated well with H&E staining. Furthermore, IRSH showed good correlation with immunostaining data obtained with anti-Ki-67 and anti-cleaved caspase-3 antibodies, whereby the L9Mc peptide inhibited cell proliferation and increased strongly apoptosis of B16F1 cells in this mouse model of melanoma primary tumors.
Seven Years of Vitrified Blastocyst Transfers: Comparison of 3 Preparation Protocols at a Single ART Center

Introduction: Frozen–thawed embryo transfers (FET) have become a standard practice to increase cumulative pregnancy rates, however, the choice of the best preparation protocol remains a matter of debate. Design: Retrospective analysis of clinical pregnancy (CPR) and live birth rate (LBR) of FET in natural cycles (NC-FET), modified natural cycles with hCG-triggered ovulation (mNC-FET), and hormonal artificial replacement (AR-FET). Materials and Methods: For natural cycles, patients were monitored by ultrasound to evaluate the dominant follicle and by urinary LH kits (NC-FET). When the endometrial thickness reached at least 7 mm and the dominant follicle 16–20 mm, hCG was administered in absence of urinary LH surge (mNC-FET). Embryo thawing and transfer was planned 7 days after LH surge or hCG administration. For the AR-FET, oral estradiol valerate was administered from day 2 of menstrual cycle until endometrial thickness reached at least 7 mm and transfer was planned after 5 days of vaginal progesterone start. Only single vitrified blastocyst transfers were included. Results: In total 2,895 transfers were performed of which 561 (19.4%) carried out with NC-FET, 1,749 (60.4%) with mNC-FET and 585 (20.2%) with AR-FET. CPRs were 32.62, 43.05, and 37.26%, respectively. LBR were 24.06, 33.56, and 25.81%, respectively. A statistically significant (p < 0.001) higher LBR for mNC-FET vs. NC-FET (OR 0.49–0.78) and AR-FET (OR 0.47–0.74) was observed. A higher ectopic pregnancy rate (p = 0.002) was observed in NC-FET (3.28%) than in AR-FET (1.83%) and mNC-FET (0.40%). A higher abortion rate (p = 0.031) in pregnancies <12 weeks was observed in AR-FET (27.52%) than in NC-FET (19.67%) and in mNC-FET (19.39%). At Post hoc analysis only female age (OR 0.91–0.95), antimullerian hormone (AMH) (OR 1.01–1.07) and mNC-FET (OR 1.39–1.98) were statically significant prognostic factors for LBRs. Conclusions: These results demonstrate a superior CPR and LBR following FET in hCG-triggered ovulation cycles compared to NC and AR-FET, a higher ectopic pregnancy rate in NC-FET and a higher abortion rate in pregnancies <12 weeks in AR-FET. However, these data need to be confirmed in randomized and prospective studies before definitive conclusions can be drawn. Clinicaltrials.gov ID: NCT03581422
The Dark Ocean Is Full of Lights

Imagine that your body could emit light whenever you needed it. You would never be afraid in the dark or at night, because you could light up the world around you. You could shoot a flashing cloud under your bed so that monsters in the darkness would be blinded, while you escape. Many animals in the ocean can actually do that; this superpower is called bioluminescence! In the open sea, about three quarters of all animals are bioluminescent, and these animals can live anywhere from the surface down to 4,000 meters deep. This light emission is an efficient way to communicate with mates, attract prey, or escape predators in the darkness of the oceans.
Characterization of microbial communities in deep groundwater from granitic rock

The microbial characteristics of deep granitic nutrient-poor groundwater from two boreholes at the Underground Research Laboratory of Atomic Energy of Canada Limited were studied. Scanning electron microscopy of the groundwater samples revealed significant numbers of bacteria of various sizes and shapes, including spherical, rod, and curved shaped. A few bacteria with appendages were also observed. Significant numbers of bacteria (~105/mL) were enumerated using acridine orange (AO) staining. An active microbial population was detected with three direct methods and it ranged from 1 to 83% of the AO count, depending on the method used. Culturable aerobic and anaerobic (including facultative) heterotrophic bacteria ranged from 0.06 to 10.2% and 0.008 to 7.35%, respectively, of the AO count. Denitrifying, N2-fixing, sulphate-reducing, and iron-precipitating bacteria were present, but no iron-oxidizing bacteria or methanogens could be detected. Tentative identification of 160 isolates using the Biolog® system .
Potential Novel Risk Factor for Breast Cancer: Toxocara canis Infection Increases Tumor Size Due to Modulation of the Tumor Immune Microenvironment

Worldwide, breast cancer is the most important type of cancer in women with regard to incidence and prevalence. Several risk factors interact to increase the probability of breast cancer development. Biological environmental contaminants such as infectious agents play a significant role in tumor development, and helminths have been recognized as cancer enhancers or inducers due to their ability to regulate the host immune response. Toxocara canis is a zoonotic and cosmopolite nematode with immuno-regulatory abilities. T. canis infection has been related to T helper type-2 cell (Th2 or type 2) and regulatory responses. Type 2 and regulatory immune responses may favor the development of comorbidities that are usually controlled or eliminated through a type 1 response such as cancer. The aim of this study was to determine whether T. canis infection alters mammary tumor growth through modulation of the immune response. Infected mice developed larger tumors. Tumor immune cell milieu analysis revealed that infection reduced the proportions of CD8+ lymphocytes and increased the proportions of F4/80+ macrophages and CD19+ B cells. These changes were accompanied by a type 2 local response represented by increased amounts of IL-4 and VEGF and a regulatory microenvironment associated with higher IL-10 levels. Thus, this study demonstrates that T. canis infection enhances tumor development and suggests that this is through modulation of the tumor immune microenvironment.
Stem Cells in Veterinary Medicine—Current State and Treatment Options

Regenerative medicine is a branch of medicine that develops methods to grow, repair, or replace damaged or diseased cells, organs or tissues. It has gained significant momentum in recent years. Stem cells are undifferentiated cells with the capability to self—renew and differentiate into tissue cells with specialized functions. Stem cell therapies are therefore used to overcome the body's inability to regenerate damaged tissues and metabolic processes after acute or chronic insult. The concept of stem cell therapy was first introduced in 1991 by Caplan, who proposed that massive differentiation of cells into the desired tissue could be achieved by isolation, cultivation, and expansion of stem cells in in vitro conditions. Among different stem cell types, mesenchymal stem cells (MSC) currently seem to be the most suitable for therapeutic purposes, based on their simple isolation and culturing techniques, and lack of ethical issues regarding their usage. Because of their remarkable immunomodulatory abilities, MSCs are increasingly gaining recognition in veterinary medicine. Developments are primarily driven by the limitations of current treatment options for various medical problems in different animal species. MSCs represent a possible therapeutic option for many animal diseases, such as orthopedic, orodental and digestive tract diseases, liver, renal, cardiac, respiratory, neuromuscular, dermal, olfactory, and reproductive system diseases. Although we are progressively gaining an understanding of MSC behavior and their mechanisms of action, some of the issues considering their use for therapy are yet to be resolved. The aim of this review is first to summarize the current knowledge and stress out major issues in stem cell based therapies in veterinary medicine and, secondly, to present results of clinical usage of stem cells in veterinary patients.
Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis

Multidrug resistant Acinetobacter baumannii is a serious healthcare threat. In fact, the Center for Disease Control recently reported that carbapenem-resistant A. baumannii is responsible for more than 8,500 infections, 700 deaths, and $281 million in healthcare costs annually in the United States with few, if any, treatment options available, leading to its designation as a pathogen of urgent concern and a priority for novel antimicrobial development. It is hypothesized that biofilms are, at least in part, responsible for the high prevalence of A. baumannii nosocomial and recurrent infections because they frequently contaminate hospital surfaces and patient indwelling devices; therefore, there has been a recent push for mechanistic understanding of biofilm formation, maturation and dispersal. However, most research has focused on A. baumannii pneumonia and bloodstream infections, despite a recent retrospective study showing that 17.1% of A. baumannii isolates compiled from clinical studies over the last two decades were obtained from urinary samples. This highlights that A. baumannii is an underappreciated uropathogen. The following minireview will examine our current understanding of A. baumannii biofilm formation and how this influences urinary tract colonization and pathogenesis.
Searching for Germplasm Resistant to Sheath Blight from the USDA Rice Core Collection

Sheath blight, caused by the fungal pathogen Rhizoctonia solani, is one of the most important and widely distributed diseases capable of infesting numerous crops including rice (Oryza sativa L.). Resistant germplasm with wide variation is essential for controlling this disease via breeding efforts, and genetic background helps design breeding strategies. We used the micro-chamber method to evaluate the USDA rice core collection, including 1794 accessions from 114 countries, for sheath blight resistance. Seventy-two molecular markers were used for genotyping. Compared with 'Jasmine 85', which has been recognized as one of the most resistant germplasm accessions, 52 accessions were significantly more resistant at the 5% level of probability, and of these 17 were more resistant at the 1% level of probability. The resistant accessions originated from 26 countries in nine geographic regions and are diversified for 13 phenotypic characteristics. The resistant accessions all belonged to the cultivated species O. sativa. Genetic analysis using 72 molecular markers revealed that 45 resistant accessions (87%) were indica type, which were further classified in two groups. Three accessions were identified as aus, two as aromatic, and one each as temperate japonica and tropical japonica. Breeders could use these findings to choose sheath blight resistant accessions for cultivar improvement.
Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars

Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana ‘Zhonglin46’ (Pe1), P. euramericana ‘Guariento’ (Pe2), P. nigra ‘N179’ (Pn1), P. deltoides ‘Danhong’ (Pd1), and P. deltoides ‘Nanyang’ (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.
Antibacterial activity of the stem bark of Boswellia dalzielii

Crude extracts of the stem bark of Boswellia dalzielli were tested for antibacterial activity. Values for the minimum inhibitory concentration (MIC) for gram-positive bacteria indicated that Staphylococcus aureus was the most susceptible, followed by Staphylococcus aureus NCTC 6570. Staphylococcus epidemidis, Bacillus cereus and the least was Bacillus megaterium. Similarly, MIC values for gram-negative bacteria showed that inhibitory activity was most pronounced for Klebsiella pneumoniae followed by Escherichia coli, Escherichia coli NCTC 10418, Proteus mirabilis and Pseudomonas aeruginosa . From the minimum bactericidal concentration (MBC) values, it was found that the bactericidal activity of both gram-positive and gram-negative bacteria followed the exact pattern of the MIC. In general, gram-negative bacteria were more susceptible than gram-negative ones. Data from viable count determination showed that microbial growth was inhibited, in both Staphylococcus aureus and Klebsiella pneumoniae when various concentrations of the crude extract were added. Journal of Pharmacy & Bioresources Vol. 2(2) 2005: 131-136
Circulating BPIFB4 Levels Associate With and Influence the Abundance of Reparative Monocytes and Macrophages in Long Living Individuals

Long-Living Individuals (LLIs) delay aging and are less prone to chronic inflammatory reactions. Whether a distinct monocytes and macrophages repertoire is involved in such a characteristic remains unknown. Previous studies from our group have shown high levels of the host defense BPI Fold Containing Family B Member 4 (BPIFB4) protein in the peripheral blood of LLIs. Moreover, a polymorphic variant of the BPIFB4 gene associated with exceptional longevity (LAV-BPIFB4) confers protection from cardiovascular diseases underpinned by low-grade chronic inflammation, such as atherosclerosis. We hypothesize that BPIFB4 may influence monocytes pool and macrophages skewing, shifting the balance toward an anti-inflammatory phenotype. We profiled circulating monocytes in 52 LLIs (median-age 97) and 52 healthy volunteers (median-age 55) using flow cytometry. If the frequency of total monocyte did not change, the intermediate CD14++CD16+ monocytes counts were lower in LLIs compared to control adults. Conversely, non-classical CD14+CD16++ monocyte counts, which are M2 macrophage precursors with an immunomodulatory function, were found significantly associated with the LLIs' state. In a differentiation assay, supplementation of the LLIs' plasma enhanced the capacity of monocytes, either from LLIs or controls, to acquire a paracrine M2 phenotype. A neutralizing antibody against the phosphorylation site (ser 75) of BPIFB4 blunted the M2 skewing effect of the LLIs' plasma. These data indicate that LLIs carry a peculiar anti-inflammatory myeloid profile, which is associated with and possibly sustained by high circulating levels of BPIFB4. Supplementation of recombinant BPIFB4 may represent a novel means to attenuate inflammation-related conditions typical of unhealthy aging.
A Unique Bellyful: Extraordinary Gut Microbes Help Herbivorous Fish Eat Seaweeds

All animals rely on a unique community of microbes to help digest food. This is especially true for plant-eating animals, which need a complex mix of gut bacteria, also known as microbes, to digest the tough plant material they eat. However, when it comes to herbivorous animals in the sea, like some fish, we know much less about the role microbes play in helping to digest food. Marine algae, better known as seaweeds, are unlike land plants in many ways, so herbivorous fish species likely have unique ways of digesting them. Therefore, we investigated the gut microbes in several herbivorous fishes in the Red Sea to see how they help fish digest algae. Surprisingly, we found that even though these fish had unique gut microbe communities, all were made up by varieties of one type of giant bacteria that appears to have evolved to help them digest their favorite algae!
A 300 Mbps 37 pJ/bit Pulsed Optical Biotelemetry

This article reports an implantable transcutaneous telemetry for a brain machine interface that uses a novel optical communication system to achieve a highly energy-efficient link. Based on an pulse-based coding scheme, the system uses sub-nanosecond laser pulses to achieve data rates up to 300 Mbps with relatively low power levels when compared to other methods of wireless communication. This has been implemented using a combination of discrete components (semiconductor laser and driver, fast-response Si photodiode and interface) integrated at board level together with reconfigurable logic (encoder, decoder and processing circuits implemented using Xilinx KCU105 board with Kintex UltraScale FPGA). Experimental validation has been performed using a tissue sample that achieves representative level of attenuation/scattering (porcine skin) in the optical path. Results reveal that the system can operate at data rates up to 300 Mbps with a bit error rate (BER) of less than 10$^{-10}$, and an energy efficiency of 37 pJ/bit. This can communicate, for example, 1,024 channels of broadband neural data sampled at 18 kHz, 16-bit with only 11 mW power consumption.