Miracle-dz/UniFAR-FTUs huggingface dataset:
GPCR receptor phosphorylation and endocytosis are not necessary to switch polarized growth between internal cues during pheromone response in S. cerevisiae

ABSTRACT Chemotactic/chemotropic cells follow accurately the direction of gradients of regulatory molecules. Many G-protein-coupled receptors (GPCR) function as chemoattractant receptors to guide polarized responses. In “a” mating type yeast, the GPCR Ste2 senses the α-cell’s pheromone. Previously, phosphorylation and trafficking of this receptor have been implicated in the process of gradient sensing, where cells dynamically correct growth. Correction is often necessary since yeast have intrinsic polarity sites that interfere with a correct initial gradient decoding. We have recently showed that when actively dividing (not in G1) yeast are exposed to a uniform pheromone concentration, they initiate a pheromone-induced polarization next to the mother–daughter cytokinesis site. Then, they reorient their growth to the intrinsic polarity site. Here, to study if Ste2 phosphorylation and internalization are involved in this process, we generated receptor variants combining three types of mutated signals for the first time: phosphorylation, ubiquitylation and the NPFX1,2D Sla1-binding motif. We first characterized their effect on endocytosis and found that these processes regulate internalization in a more complex manner than previously shown. Interestingly, we showed that receptor phosphorylation can drive internalization independently of ubiquitylation and the NPFX1,2D motif. When tested in our assays, cells expressing either phosphorylation or endocytosis-deficient receptors were able to switch away from the cytokinesis site to find the intrinsic polarity site as efficiently as their WT counterparts. Thus, we conclude that these processes are not necessary for the reorientation of polarization.
Comparison Between Surgical and Nonsurgical Treatment for Primary Patellar Dislocations in Adolescents: A Systematic Review and Meta-analysis of Comparative Studies

Background: Whether surgical or nonsurgical management is more appropriate for primary patellar dislocations (PPDs) in adolescents (younger than 18 years) remains controversial. Purpose: To compare the clinical outcomes of surgical versus nonsurgical treatment for adolescents and children with PPDs. Study Design: Systematic review; Level of evidence, 3. Methods: There were 2 reviewers who independently searched the PubMed, Embase, Ovid, and Cochrane databases for English-language studies of randomized controlled trials (RCTs), quasi-RCTs, and observational studies comparing surgical with nonsurgical treatment for PPDs. The primary outcomes were redislocations, the Kujala score, and the Knee injury and Osteoarthritis Outcome Score (KOOS), and the secondary outcome was subsequent surgery. Results: A total of 6 studies were included in our systematic review and meta-analysis. Among patients younger than 18 years, surgery was associated with a lower redislocation rate compared with nonsurgical treatment within 5 years of treatment (risk ratio [RR], 0.58 [95% CI, 0.37-0.91]; P = .02; I 2 = 47%) but not beyond 5 years (RR, 0.80 [95% CI, 0.59-1.07]; P = .14; I 2 = 34%). However, surgery resulted in worse Kujala and KOOS scores compared with nonsurgical treatment. Yet, the treatment difference between the 2 groups tended to decrease over time. Conclusion: The available evidence suggests that for adolescents with PPDs, surgery was superior to nonsurgical treatment in the short term to reduce the redislocation rate but resulted in poorer outcomes of knee function based on the Kujala and KOOS scores. However, the superiority of either surgical or nonsurgical treatment in adolescents did not appear to persist in the long term.
Addressing cancer signal transduction pathways with antisense and siRNA oligonucleotides

Abstract Signal transduction pathways play key roles in the initiation, progression and dissemination of cancer. Thus, signaling molecules are attractive targets for cancer therapeutics and enormous efforts have gone into the development of small molecule inhibitors of these pathways. However, regrettably, there has been only moderate progress to date, primarily in connection with the RAS signaling pathway. Oligonucleotide-based drugs potentially offer several advantages for addressing signaling pathways, including their exquisite selectivity and their ability to exploit both enzymatic and nonenzymatic targets. Nonetheless, there are problems inherent in the oligonucleotide approach, not the least being the challenge of effectively delivering these complex molecules to intracellular sites within tumors. This survey article will provide a selective review of recent studies where oligonucleotides were used to address cancer signaling and will discuss both positive aspects and limitations of those studies. This will be set in the context of an overview of various cancer signaling pathways and small molecule approaches to regulate those pathways. The survey will also evaluate the challenges and opportunities implicit in the oligonucleotide-based approach to cancer signaling and will point out several possibilities for future research.
Reproduction and Ecology of the Atlantic Stingray, Dasyatis sabina, in Florida Coastal Lagoons

ROMER, A. S. 1962. The vertebrate body. 3rd ed. W. B. Saunders Co., Philadelphia, Pennsylvania. SIMPSON, T. H. , AND C. S. WARDLE. 1967. A seasonal cycle of the testis of the spurdog, Squalus acanthias, and the sites of 3B-hydroxysteroid dehydrogenase activity. J. Mar. Biol. Assoc. U.K. 47:699-708. STANLEY, H. P. 1963. Urogenital morphology in the chimaeroid fish Hydrolagus colliei (Lay and Bennett). J. Morph. 112:99-127. hark, Cetorhinus maximus (Gunner). Philos. Trans. . Soc. Lond. , Ser. B. Biol. Sci. 234:247-316. EL INGER, J. 1965. Studes de la spermatogen se hez Scyliorhinus caniculus (L.). Description, donees histochimiques, variations normales et experi entals. Z Zellforsch. Mikroskop. Anat. 67:65373.
Taxonomic status of Brucepattersonius albinasus (Rodentia: Sigmodontinae)

Molecular (cytochrome b) comparisons between topotypical specimens of Brucepattersonius griserufescens and the holotype of B. albinasus, both described from the same locality in southeastern Brazil, reveal a very low estimate of genetic distance, equivalent to those obtained in comparisons between haplotypes of B. griserufescens. Only six variable sites, five transitions and one transversion, were found among the 1040 bp of all haplotypes. These findings, together with a re-evaluation of the morphological characters on which the distinction between the two nominal forms was based, indicate that only one evolutionary lineage is represented, which must bear the name B. griserufescens, with B. albinasus as a junior synonym.
NEW PYRAN OF AN ENDOPHYTIC FUNGUS Fusarium sp. ISOLATED FROM THE LEAVES OF BROTOWALI (Tinaspora crispa)

Endophytes are microorganisms that reside asymptomatically in the tissues of higher plants and are relatively unstudied and a promising source of novel organic natural metabolites exhibiting a variety of biological activities. As a part of our systematic search for new bioactive lead structures from endophytic, the endophytic fungus Fusarium sp. isolated from the leaves of Brotowali (Tinaspora crispa), was cultured for isolation of metabolite. The endophytic fungus was cultivated on 6 L of Potatos Dextose Broth (PDB) medium at room temperature (no shaking) for 8 weeks. The cultures were then extracted with ethyl acetate to afford 9.4 g of residue after removal of the solvent under reduced pressure. The extract was separated into the fractions by column chromatography (CC) on silica gel. The fractions were further separated by silica gel column chromatography to give one compound. The molecular structure was established on the basis of spectroscopic analysis including UV, IR, 1 H-NMR, 13 C-NMR, HMQC, HMBC, COSY, and MS. The compound was determined as a new pyran.
Acquisition, identification and analysis of an interspecific Capsicum hybrid (C. annuum × C. chinense)

Summary Using an embryo rescue technique, we obtained an F1 plantlet whose female parent was a purple chilli pepper (Capsicum annuum 7033) and whose male parent was a green chilli pepper (C. chinense 7020). We verified the origin of this interspecific hybrid using a peroxidase isozyme assay and random amplified polymorphic DNA (RAPD) markers. Most of the morphological features of the F1 plant, particularly the purple colour of its foliage, flowers and immature fruit, were intermediate between those of its parents. Cytological analysis indicated that the meiotic chromosomes of the pollen mother cells of the F1 plant exhibited abnormal behaviour, resulting in a marked reduction in the proportion of fertile pollen compared to both its parents. Sequence analysis of the internal transcribed spacer of nuclear ribosomal DNA demonstrated that, compared to the parental sequences, the F1 hybrid had 186 polymorphic sites, 139 of which (74.7%) were inherited from the male parent, and 23 (12.4%) were inherited from the female parent, and 24 (12.9%) were transversions or base pair mutations. Therefore, our morphological and cytological observations, as well as isozyme and molecular marker analyses confirmed that the F1 plant was a genuine interspecific hybrid that had inherited more genetic information from its male parent than from its female parent. This work will help locate purple colour-related genes and the breeding of pepper cultivars containing higher concentrations of anthocyanin and capsaicin.
AFLP identification and characterization of Yongxuan 56, a new line of Biqi Chinese bayberry

Yongxuan 56, a new line of Biqi bayberry cultivar with bigger fruit and better fruit quality, was selected from a bayberry orchard located in Jiangbei district of Ningbo, Zhejiang province. Its average fruit weight and diameter reaches (14.25 ± 1.56) g and (3.00 ± 0.11) cm, significantly greater than that of the maternal cultivar Biqi (9.05 ± 1.39) g and (2.55 ± 0.09) cm. Both the content of soluble sugars and organic acids are higher in the fruit of the new line than those of the original cultivar Biqi, being (125.97±4.25) and (10.04±0.32) mg/mL juice versus (106.90±3.29) and 8.44±0.19 mg/mL juice. Results of 4 years investigation on the botanical characteristics and fruit quality proved that its bigger fruit and higher fruit quality are stable. Based on AFLP analysis, it is suggested that Yongxuan 56 is a genetically new line.
The Antioxidant Status of Soybean (Glycine max) Leaves Grown Under Natural CO2 Enrichment in the Field

The effects of progressively higher CO2 levels on the foliar antioxidant status were studied by growing soybean (Glycine max Merrill cv. Cresir) plants at decreasing distances from natural CO2 sources of geothermal origin in central Italy. When compared with neighbouring controls grown under normal CO2 concentration (C), soybean leaves grown at 2 × C, 7 × C and more than 20 × C showed a substantial reduction in the size of ascorbate pool and in the activity of Cu,Zn-superoxide dismutase; both the content of ascorbic acid and the activity of ascorbate peroxidase declined at 2 × C and 7 × C and recovered to the control values at 20 × C. The foliar titre of glutathione disulfide and the activities of glutathione disulfide reductase and Mn-superoxide dismutase progressively increased as CO2 concentration increased in ambient air. The results obtained suggest that the immanent risk of dioxygen toxicity associated with photosynthetic electron flow could be reduced in the presence of high CO2 levels. On the other hand, depending on both the CO2 exposure regimes and the cell compartment considered, high CO2 could promote oxidative processes which cause GSH oxidation and require an enhanced cellular ability to scavenge superoxide anion and hydrogen peroxide.
A Review of RNA Secondary Structure Prediction Algorithms

RNA secondary structure prediction is one of the most important fields in computational molecular biology.The method to predict RNA secondary structure is introduced,including the mathematic models,main algorithms and softwares.Then seven main softwares are tested and compared detailedly with some groups of tRNA and RNase P.It showed that Pfold performed better than others when several homologous RNA sequences were predicted.At last some vital aspects that may be conducted in the future investigations are discussed.
Reproductive management of seasonal calving dairy herds

Background: Seasonal calving herds account for around a fifth of dairy farms in the UK (AHDB 2016). Their structure allows focused farm management and seasonal labour requirements, as well as the opportunity to maximise the conversion of grazed grass into milk. However, their economic success is underpinned by a requirement for optimal reproductive management, and for this reason a thorough understanding of how to approach fertility in these herds is essential for veterinary surgeons involved in their management. Aim of the article: This article explains the concept of seasonal calving systems, the impacts of poor fertility, the key performance indicators used to monitor performance in clinical practice, and the key areas where improvements can be made.
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster

The CRISPR/Cas system has stood in the center of attention in the last few years as a revolutionary gene editing tool with a wide application to investigate gene functions. However, the labor-intensive workflow requires a sophisticated pre-experimental and post-experimental analysis, thus becoming one of the hindrances for the further popularization of practical applications. Recently, the increasing emergence and advancement of the in silico methods play a formidable role to support and boost experimental work. However, various tools based on distinctive design principles and frameworks harbor unique characteristics that are likely to confuse users about how to choose the most appropriate one for their purpose. In this review, we will present a comprehensive overview and comparisons on the in silico methods from the aspects of CRISPR/Cas system identification, guide RNA design, and post-experimental assistance. Furthermore, we establish the hypotheses in light of the new trends around the technical optimization and hope to provide significant clues for future tools development.
Micro Three-Dimensional Neuronal Cultures Generate Developing Cortex-Like Activity Patterns

Studies aimed at neurological drug discovery have been carried out both in vitro and in vivo. In vitro cell culture models have showed potential as drug testing platforms characterized by high throughput, low cost, good reproducibility and ease of handling and observation. However, in vitro neuronal culture models are facing challenges in replicating in vivo-like activity patterns. This work reports an in vitro culture technique that is capable of producing micro three-dimensional (μ3D) cultures of only a few tens of neurons. The μ3D cultures generated by this method were uniform in size and density of neurons. These μ3D cultures had complex spontaneous synchronized neuronal activity patterns which were similar to those observed in the developing cortex and in much larger 3D cultures, but not in 2D cultures. Bursts could be reliably evoked by stimulation of single neurons. Synchronized bursts in μ3D cultures were abolished by inhibitors of glutamate receptors, while inhibitors of GABAA receptors had a more complex effect. This pharmacological profile is similar to bursts in neonatal cortex. Since large numbers of reproducible μ3D cultures can be created and observed in parallel, this model of the developing cortex may find applications in high-throughput drug discovery experiments.
Extracellular Vesicles Derived From Apoptotic Cells: An Essential Link Between Death and Regeneration

Apoptosis is a universal and continuous event during tissue development, restoration, repair, and regeneration. Mounting evidence has demonstrated that apoptosis is essential for the activation of tissue regeneration. However, the underlying mechanism remains elusive. A striking development in recent years comes from research on extracellular vesicles (EVs) derived from apoptotic cells. During apoptosis, cells secrete vesicles of various sizes containing various components. Apoptotic cell-derived EVs (ApoEVs) have been found to transit to neighboring cells or cells in distant tissues through the circulation. These vesicles could act as containers to transmit the nucleic acid, protein, and lipid signals to target cells. ApoEVs have been shown to promote regeneration in the cardiovascular system, skin, bone, muscle, kidney, etc. Moreover, several specific signaling pathways mediating the anabolic effects of ApoEVs have been classified. In this review, we comprehensively discussed the latest findings on the function of ApoEVs in tissue regeneration and disease prevention. These findings may reveal unexpected clues regarding the regulatory network between cell death and tissue regeneration and suggest novel targets for regenerative medicine. The findings discussed here also raise the question whether and to what extent ApoEVs contribute to embryonic development. This question is all the more urgent because the exact functions of apoptotic events during numerous developmental processes are still largely unclear.
Social Context Influence on Urban Gardener Perceptions of Pests and Management Practices

Community gardens are important urban green spaces with a variety of social and ecological benefits, one of which is access to healthy food. Similar to rural agriculture, the quantity and quality of the food produced can be compromised by pest damage. In fact, many urban gardeners report crop damages caused by vertebrate and invertebrate pests. Yet, because the food produced in community gardens is mostly for self-consumption and thus not under market quality standards, the damage thresholds and the point when gardeners perceive a pest problem and how they decide to manage it, may greatly vary from gardener to gardener. Here, we investigated how socio-demographic factors and experience affect whether gardeners report having a pest problem and which pest management practices they use. We surveyed 187 gardeners from 18 different urban community gardens in three counties in the California central coast, USA. We also collected information about gardener socio-demographic factors (age, gender, ethnicity), as well as education, and years of experience in agriculture. The majority of gardeners reported having pests in their plots but their ethnicity, the amount of time they spend in the gardens, and whether they work in agricultural-related employment or not influenced the likelihood of reporting pests. We found that the majority of gardeners use curative, non-synthetic practices for managing pests, but that some use preventive practices and some don't do anything to control pests. The likelihood of using practices that are curative depended on gardeners' ethnicity, the amount of time they spend in the gardeners, and their gender. Our results suggest that the agricultural knowledge of urban community gardeners and the practices they use varies greatly and that, in order to be successful, extension programs may need to take this diversity into account when promoting the agroecological paradigm in urban agricultural (UA) systems.
Optical Coherence Tomography Angiography Reveals Distinct Retinal Structural and Microvascular Abnormalities in Cerebrovascular Disease

Cerebrovascular disease (CeVD) is one of the leading global causes of death and severe disability. To date, retinal microangiopathy has become a reflection of cerebral microangiopathy, mirroring the vascular pathological modifications in vivo. To evaluate the retinal structure and microvasculature in patients with CeVD, we conducted a cross-sectional study in Zhongshan Ophthalmic Center and Department of Neurology of Third Affiliated Hospital, Sun Yat-sen University using optical coherence tomography angiography (OCTA). CeVD patients (n = 121; 238 eyes) and healthy controls (n = 44; 57 eyes) were included in the analysis. The CeVD group showed significant thinning of the peripapillary retinal nerve fiber layer (pRNFL) thickness in the temporal and nasal quadrants, and thinning of the macular ganglion cell-inner plexiform layer (GC-IPL) in the inferior quadrant, while macular microvasculature reduction was prominent in all nine quadrants. There were significant correlations between OCTA parameters, visual acuity, and transcranial doppler parameters in the CeVD group. The specific structural parameters combining microvasculature indices showed the best diagnostic accuracies (AUC = 0.918) to discriminate CeVD group from healthy controls. To conclude, we proved that OCTA reveals specific patterns of retinal structural changes and extensive macular microvascular changes in CeVD. Additionally, these retinal abnormalities could prove useful disease biomarkers in the management of individuals at high risk of debilitating complications from a cerebrovascular event.
Dynamic Arterial Elastance During Experimental Endotoxic Septic Shock: A Potential Marker of Cardiovascular Efficiency

Dynamic arterial elastance (Eadyn), the ratio between pulse pressure variation (PPV) and stroke volume variation (SVV), has been suggested as a dynamic parameter relating pressure and flow. We aimed to determine the effects of endotoxic septic shock and hemodynamic resuscitation on Eadyn in an experimental study in 18 New Zealand rabbits. Animals received placebo (SHAM, n = 6) or intravenous lipopolysaccharide (E. Coli 055:B5, 1 mg⋅kg–1) with or without (EDX-R, n = 6; EDX, n = 6) hemodynamic resuscitation (fluid bolus of 20 ml⋅kg–1 and norepinephrine for restoring mean arterial pressure). Continuous arterial pressure and aortic blood flow measurements were obtained simultaneously. Cardiovascular efficiency was evaluated by the oscillatory power fraction [%Osc: oscillatory work/left ventricular (LV) total work] and the energy efficiency ratio (EER = LV total work/cardiac output). Eadyn increased in septic animals (from 0.73 to 1.70; p = 0.012) and dropped after hemodynamic resuscitation. Eadyn was related with the %Osc and EER [estimates: −0.101 (−0.137 to −0.064) and −9.494 (−11.964 to −7.024); p < 0.001, respectively]. So, the higher the Eadyn, the better the cardiovascular efficiency (lower %Osc and EER). Sepsis resulted in a reduced %Osc and EER, reflecting a better cardiovascular efficiency that was tracked by Eadyn. Eadyn could be a potential index of cardiovascular efficiency during septic shock.
On the Role of Platelet-Generated Amyloid Beta Peptides in Certain Amyloidosis Health Complications

As do many other immunity-related blood cells, platelets release antimicrobial peptides that kill bacteria, fungi, and even certain viruses. Here we review the literature suggesting that there is a similarity between the antimicrobials released by other blood cells and the amyloid-related Aβ peptide released by platelets. Analyzing the literature, we also propose that platelet-generated Aβ amyloidosis may be more common than currently recognized. This systemic Aβ from a platelet source may participate in various forms of amyloidosis in pathologies ranging from brain cancer, glaucoma, skin Aβ accumulation, and preeclampsia to Alzheimer’s disease and late-stage Parkinson’s disease. We also discuss the advantages and disadvantages of specific animal models for studying platelet-related Aβ. This field is undergoing rapid change, as it evaluates competing ideas in the light of new experimental observations. We summarized both in order to clarify the role of platelet-generated Aβ peptides in amyloidosis-related health disorders, which may be helpful to researchers interested in this growing area of investigation.