Miracle-dz/UniFAR-FTUs huggingface dataset:
Lactoferrin and hematoma detoxification after intracerebral hemorrhage.

This review discusses the role of lactoferrin (LTF) in detoxifying hematoma after intracerebral hemorrhage (ICH). Subsequent to ICH, neutrophils enter the ICH-affected brain, where they release various granule content, including LTF. LTF is an iron-binding glycoprotein that binds Fe3+ with high affinity. Unlike other iron binding proteins, LTF can retain Fe3+ at the low pH associated with inflamed tissue. LTF's ability to sequester Fe3+ is of particular importance to ICH pathogenesis, as large quantities of free iron, which is pro-oxidative and pro-inflammatory are generated in the ICH-affected brain due to blood hemolysis. LTF delivered to ICH-affected brain, either as therapeutic agent or through infiltrated PMNs (cells containing high levels of LTF), could benefit ICH pathogenesis. LTF is a protein with a high isoelectric point (8.7), property that enables it to binding to negatively charged apoptotic cells or proteins. Here, LTF could act as a bridging molecule that couples the apoptotic cells to LTF receptors on the cellular membranes of microglia/macrophages to facilitates the efferocytosis/erythrophagocytosis of apoptotic cells and damaged red blood cells. Thus, by virtue of sequestrating iron and facilitating efferocytosis, LTF may contribute to hematoma detoxification and hematoma/inflammation resolution after ICH.
Chloroplast structural and functional changes as biomarkers of heavy metal contamination

Chloroplast ultra-structural changes of Pisum sativum L were detected using the transmission electron microscopy. This work deals with studies of chloroplast structure responses to a high content of copper (250 μmМ) and zinc (400 μmМ). Data on changes in the structure of chloroplasts in particular, heterogeneity in the grain thylakoid packing, increase of interthylakoid gaps and thickness of chloroplast grain thylakoids in comparison with controls were obtained. The results of studies on structural and functional chloroplasts changes offer challenges for their use as markers for an early diagnostics of abiotic stress effects and in biotechnological studies to produce novel advanced varieties of crops resistant to stress.
An Unexpectedly Complex Mitoribosome in Andalucia godoyi, a Protist with the Most Bacteria-like Mitochondrial Genome

Abstract The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly accepted view assumes that M-mtRPs compensate for structural destabilization of mt-rRNA resulting from its evolutionary remodeling. Since most experimental information on mitoribosome makeup comes from eukaryotes having derived mitochondrial genomes and mt-rRNAs, we tested this assumption by investigating the mitochondrial translation machinery of jakobids, a lineage of unicellular protists with the most bacteria-like mitochondrial genomes. We report here proteomics analyses of the Andalucia godoyi small mitoribosomal subunit and in silico transcriptomic and comparative genome analyses of four additional jakobids. Jakobids have mt-rRNA structures that minimally differ from their bacterial counterparts. Yet, with at least 31 small subunit and 44 large subunit mtRPs, the mitoriboproteome of Andalucia is essentially as complex as that in animals or fungi. Furthermore, the relatively high conservation of jakobid sequences has helped to clarify the identity of several mtRPs, previously considered to be lineage-specific, as divergent homologs of conserved M-mtRPs, notably mS22 and mL61. The coexistence of bacteria-like mt-rRNAs and a complex mitoriboproteome refutes the view that M-mtRPs were ancestrally recruited to stabilize deviations of mt-rRNA structural elements. We postulate instead that the numerous M-mtRPs acquired in the last eukaryotic common ancestor allowed mt-rRNAs to pursue a broad range of evolutionary trajectories across lineages: from dramatic reduction to acquisition of novel elements to structural conservatism.
CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

Abstract The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.
Proteinoid Nanocapsules as Drug Delivery System for Improving Antipsychotic Activity of Risperidone

Risperidone (RSP) is an atypical antipsychotic drug widely used to treat schizophrenia and bipolar disorder. Nanoparticles (NPs) are being developed as in vivo targeted drug delivery systems, which cross the blood-brain barrier and improve pharmacokinetics and drug effectiveness. Here, biodegradable proteinoids were synthesized by thermal step-growth polymerization from the amino acids l-glutamic acid, l-phenylalanine and l-histidine and poly (l-lactic acid). Proteinoid NPs containing RSP were then formed by self-assembly, overcoming the insolubility of the drug in water, followed by PEGylation (poly ethylene glycol (PEG) conjugation to increase the stability of the NPs in the aqueous continuous phase. These NPs are biodegradable owing to their peptide and ester moieties. They were characterized in terms of diameter, size distribution, drug loading, and long-term storage. Behavioral studies on mice found enhanced antipsychotic activity compared to free RSP.
Fermentation profiles of the yeast Brettanomyces bruxellensis in d‐xylose and l‐arabinose aiming its application as a second‐generation ethanol producer

The yeast Brettanomyces bruxellensis is able to ferment the main sugars used in first‐generation ethanol production. However, its employment in this industry is prohibitive because the ethanol productivity reached is significantly lower than the observed for Saccharomyces cerevisiae. On the other hand, a possible application of B. bruxellensis in the second‐generation ethanol production has been suggested because this yeast is also able to use d‐xylose and l‐arabinose, the major pentoses released from lignocellulosic material. Although the latter application seems to be reasonable, it has been poorly explored. Therefore, we aimed to evaluate whether or not different industrial strains of B. bruxellensis are able to ferment d‐xylose and l‐arabinose, both in aerobiosis and oxygen‐limited conditions. Three out of nine tested strains were able to assimilate those sugars. When in aerobiosis, B. bruxellensis cells exclusively used them to support biomass formation, and no ethanol was produced. Moreover, whereas l‐arabinose was not consumed under oxygen limitation, d‐xylose was only slightly used, which resulted in low ethanol yield and productivity. In conclusion, our results showed that d‐xylose and l‐arabinose are not efficiently converted to ethanol by B. bruxellensis, most likely due to a redox imbalance in the assimilatory pathways of these sugars. Therefore, despite presenting other industrially relevant traits, the employment of B. bruxellensis in second‐generation ethanol production depends on the development of genetic engineering strategies to overcome this metabolic bottleneck.
Altered Motor Excitability in Patients With Diffuse Gliomas Involving Motor Eloquent Areas: The Impact of Tumor Grading.

BACKGROUND Diffuse gliomas have an increased biological aggressiveness across the World Health Organization (WHO) grading system. The implications of glioma grading on the primary motor cortex (M1)-corticospinal tract (CST) excitability is unknown. OBJECTIVE To assess the excitability of the motor pathway with navigated transcranial magnetic stimulation (nTMS). METHODS Retrospective cohort study of patients admitted for surgery with diffuse gliomas within motor eloquent areas. Demographic, clinical, and nTMS-related variables were collected. The Cortical Excitability Score (CES 0 to 2 according to the number of abnormal interhemispheric resting motor threshold (RMT) ratios) was calculated for patients where bilateral upper and lower limb mapping was performed. RESULTS A total of 45 patients were included: 9 patients had a low-grade glioma and 36 patients had a high-grade glioma. The unadjusted analysis revealed an increase in the latency of the motor evoked potential of the lower limb with an increase of the WHO grade (P = .038). The adjusted analysis confirmed this finding (P = .013) and showed a relation between the increase in the WHO and a decreased RMT (P = .037) of the motor evoked responses in the lower limb. When CES was calculated, an increase in the score was related with an increase in the WHO grade (unadjusted analysis-P = .0001; adjusted analysis-P = .001) and in isocitrate dehydrogenase (IDH) wild-type tumors (unadjusted analysis-P = .020). CONCLUSION An increase in the WHO grading system and IDH wild-type tumors are associated with an abnormal excitability of the motor eloquent areas in patients with diffuse gliomas.
Screening and Reverse-Engineering of Estrogen Receptor Ligands as Potent Pan-Filovirus Inhibitors.

Filoviridae, including Ebola (EBOV) and Marburg (MARV) viruses, are emerging pathogens that pose a serious threat to public health. No agents have been approved to treat filovirus infections, representing a major unmet medical need. The selective estrogen receptor modulator (SERM) toremifene was previously identified from a screen of FDA-approved drugs as a potent EBOV viral entry inhibitor, via binding to EBOV glycoprotein (GP). A focused screen of ER ligands identified Ridaifen-B as a potent dual inhibitor of EBOV and MARV. Optimization and reverse-engineering to remove ER activity led to a novel compound 30 showing potent inhibition against infectious EBOV Zaire (0.09 µM) and MARV (0.64 µM). Mutagenesis studies confirmed that inhibition of EBOV viral entry is mediated by direct interaction with GP. Importantly, compound 30 displayed broad-spectrum anti-filovirus activity against Bundibugyo, Tai Forest, Reston, and Měnglà viruses, and is the first sub-micromolar antiviral agent reported for some of these strains, therefore warranting further development as a pan-filovirus inhibitor.
Effect of Satiation on Activity Patterns in Sceloporus virgatus

Comparaison de l'activite de S.virgatus avant et apres la satiete et intra et intersexes.Les males rassasies passent une plus grande partie de leur temps en activite sociale et se deplacent a des distances plus grandes que les males non rassasies.les auteurs interpretent ces resultats par rapport a l'effort reproductif
Prevalence of gestational diabetes mellitus in Argentina according to the Latin American Diabetes Association (ALAD) and International Association of Diabetes and Pregnancy Study Groups (IADPSG) diagnostic criteria and the associated maternal-neonatal complications

Abstract In Argentina, gestational diabetes mellitus (GDM) is diagnosed by the Latin American Diabetes Association (ALAD) diagnostic criterion. In this work, we investigated GDM prevalence according to the ALAD and IADPSG diagnostic criteria, evaluated maternal and fetal outcomes and assessed whether fasting glycemia between 92–99 mg/dL was associated with increased risk of macrosomia and maternal obesity/overweight in an Argentine cohort of pregnant women. GDM prevalence was 9.8% with the ALAD diagnostic criterion and 25% considering the IADPSG criterion. Increased prevalence of maternal obesity/overweight was observed in patients with fasting glycemia over 99 mg/dL. A population of high metabolic risk is identified by the ALAD criterion.
Field detection of multiple RNA viruses/viroids in apple using a CRISPR/Cas12a‐based visual assay

Summary Co‐infection of apple trees with several viruses/viroids is common and decreases fruit yield and quality. Accurate and rapid detection of these viral pathogens helps to reduce losses and prevent virus spread. Current molecular detection assays used for apple viruses require specialized and expensive equipment. Here, we optimized a CRISPR/Cas12a‐based nucleic acid detection platform for the diagnosis of the most prevalent RNA viruses/viroid in apple, namely Apple necrotic mosaic virus (ApNMV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple scar skin viroid (ASSVd). We detected each RNA virus/viroid directly from crude leaf extracts after simultaneous multiplex reverse transcription‐recombinase polymerase amplification (RT‐RPA) with high specificity. Positive results can be distinguished by the naked eye via oligonucleotide‐conjugated gold nanoparticles. The CRISPR/Cas12a‐RT‐RPA platform exhibited comparable sensitivity to RT‐qPCR, with limits of detection reaching 250 viral copies per reaction for ASPV and ASGV and 2500 copies for the others. However, this protocol was faster and simpler, requiring an hour or less from leaf harvest. Field tests showed 100% agreement with RT‐PCR detection for 52 samples. This novel Cas12a‐based method is ideal for rapid and reliable detection of apple viruses in the orchard without the need to send samples to a specialized laboratory.
Comparison of 2-Year Outcomes between Intravitreal Ranibizumab and Intravitreal Aflibercept for Diabetic Macular Edema with “Treat-and-Extend” Regimen—Its Usefulness and Problems

Background: To compare the effectiveness of intravitreal ranibizumab (IVR) and intravitreal aflibercept (IVA) performed with the treat-and-extend (TAE) regimen on eyes with diabetic macular edema (DME). Patients and methods: This is a retrospective study of 125 eyes of 125 treatment-naïve DME patients who received anti-VEGF injections at three consecutive monthly intervals as the loading phase. The changes in the best-corrected visual acuity (BCVA), central retinal thickness (CRT), diabetic retinopathy severity scale (DRSS), and total injection numbers were compared between the two anti-VEGF agents. Results: Among 125 eyes, 26 eyes completed the treatment with the TAE regimen for 24 months (20.8%). Thirteen eyes of 13 patients (mean age, 70.9 ± 6.0 years) received intravitreal injections of 0.5 mg ranibizumab, and 13 eyes of 13 patients (65.9 ± 8.6 years) received 2 mg aflibercept. No significant differences were detected in the baseline demographics. At 24 months, BCVA was significantly improved in both groups; from 0.31 ± 0.19 to 0.10 ± 0.12 logMAR units for IVR and 0.41 ± 0.19 to 0.16 ± 0.28 logMAR units for IVA (p = 1.29 × 10−9). CRT was significantly reduced in both groups; 440.9 ± 69.3 to 307.5 ± 66.4 μm for IVR and 473.9 ± 71.5 to 317.8 ± 71.2 μm for IVA (p = 3.55 × 10−9). No significant differences were detected in the improvements of BCVA, CRT in both groups, and the total injection numbers for 24 months (11.0 ± 1.2 for the IVA group and 12.0 ± 1.0 the IVR group). DRSS was significantly improved in both groups (p = 0.0004 for IVR and p = 0.009 for IVA). Conclusion: No significant differences were detected in the improvements of BCVA or CRT and injection numbers between the IVR and IVA groups treated with the TAE regimen. These results indicate that the results of the treatment with both agents with the TAE regimen were equally effective, but only 20.8% of patients completed 24 months of continuous treatment with the TAE regimen. Synopsis: There are no significant differences regarding effectiveness between the IVR and IVA groups treated with the TAE regimen for DME eyes.
Association between tumor mutation profile and clinical outcomes among Hispanic Latina women with triple-negative breast cancer

Triple-negative breast cancer (TNBC) represents 15%–20% of all breast cancer types. It is more common among African American (AA) and Hispanic-Latina (HL) women. The biology of TNBC in HL women has been poorly characterized, but some data suggest that the molecular drivers of breast cancer might differ. There are no clinical tools to aid medical oncologists with decisions regarding appropriate individualized therapy, and no way to predict long-term outcomes. The aim of this study was to characterize individual patient gene mutation profiles and to identify the relationship with clinical outcomes. We collected formalin-fixed paraffin-embedded tumors (FFPE) from women with TNBC. We analyzed the gene mutation profiles of the collected tumors and compared the results with individual patient’s clinical histories and outcomes. Of 25 patients with TNBC, 24 (96%) identified as HL. Twenty-one (84%) had stage III–IV disease. The most commonly mutated genes were TP53, NOTCH1, NOTCH2, NOTCH3, AKT, MEP3K, PIK3CA, and EGFR. Compared with other international cancer databases, our study demonstrated statistically significant higher frequencies of these genes among HL women. Additionally, a worse clinical course was observed among patients whose tumors had mutations in NOTCH genes and PIK3CA. This study is the first to identify the most common genetic alterations among HL women with TNBC. Our data strongly support the notion that molecular drivers of breast cancer could differ in HL women compared with other ethnic backgrounds. Therefore, a deeper understanding of the biological mechanisms behind NOTCH gene and PIK3CA mutations may lead to a new treatment approach.
One Size Does Not Fit All: A Grounded Theory and Online Survey Study of Developer Preferences for Security Warning Types

A wide range of tools exist to assist developers in creating secure software. Many of these tools, such as static analysis engines or security checkers included in compilers, use warnings to communicate security issues to developers. The effectiveness of these tools relies on developers heeding these warnings, and there are many ways in which these warnings could be displayed. Johnson et al. [46] conducted qualitative research and found that warning presentation and integration are main issues. We built on Johnson et al.'s work and examined what developers want from security warnings, including what form they should take and how they should integrate into their workflow and work context. To this end, we conducted a Grounded Theory study with 14 professional software developers and 12 computer science students as well as a focus group with 7 academic researchers to gather qualitative insights. To back up the theory developed from the qualitative research, we ran a quantitative survey with 50 professional software developers. Our results show that there is significant heterogeneity amongst developers and that no one warning type is preferred over all others. The context in which the warnings are shown is also highly relevant, indicating that it is likely to be beneficial if IDEs and other development tools become more flexible in their warning interactions with developers. Based on our findings, we provide concrete recommendations for both future research as well as how IDEs and other security tools can improve their interaction with developers.
The chromosome numbers of Georgian earthworms (Oligochaeta: Lumbricidae)

The data on chromosome numbers (somatic and basic) characteristic to species and subspecies of earthworms (Lumbricidae) of Georgia (Caucasus region) are summarized. Four values of basic chromosome number (11, 15, 17, 18) while 6 values of somatic number (22, 30, 34, 36, 72, 108) are registered in 19 species and subspecies studied. The diploid karyotypes dominate over polyploid karyotypes. It is supposed that the modal numbers, somatic 2n=36 and basic n=18, are evolutionarily initial on the basis of which the formation of the main part of species and subspecies of earthworms have proceeded in Georgia. Polyploidy did not represent the main evolutionary mechanism of the origin of species in Georgia (and the whole Caucasus).
Practical Implications of Malolactic Fermentation: A Review

Malolactic fermentation (MLF) is discussed in terms of its effect on wine quality and methods currently available for its control. Benefits of MLF include the lowering of acidity in high acid wines, enhancement of sensory characteristics through bacterial activity, and enhanced microbiological stability. Undesirable effects include the excessive reduction in acidity of high pH wines leading to risk of spoilage, production of undesirable flavors, color changes, and formation of amines. Methods of control involve stimulation of indigenous flora, inoculation of bacteria (either pure cultures or from wines already undergoing MLF), use of immobilized bacterial cells or enzymes, and practical measures to inhibit bacterial growth.
Capture of rotifers by Acaulopage pectospora, and further evidence of its similarity to Zoophagus insidians

Acaulopage pectospora is a nematode-trapping zoopagaceous fungus in which the hyphae bear a number of short lateral branches (ca 10-25 tm long, 2.5-3.0 Am wide) as trapping organs. Each branch terminates in a small, globose knob from which an adhesive is squeezed out to capture nematodes (Drechsler, 1962). This species is unique in the genus Acaulopage in that all other known species capture amoebae using the entire surface of their undifferentiated hyphae. The extremely large elongated conidia (ca 180-240 x 7-14 ,um) are also exceptional for the genus. Recently, Saikawa and Morikawa (1985) reported several ultrastructural aspects of the fungus as follows: (1) the trap's cytoplasm was occupied by large electron-dense vesicles (0.4-0.8 ,um) before secretion of the adhesive; (2) the secreted adhesive derived from the large vesicles had a high electron density and contained a number of bubbles; (3) the cell walls of the traps became doubled after the secretion of the adhesive and an aliquot of the adhesive remained in the intervening spaces between the outer and newly-formed inner cell walls; (4) the outer wall of the terminal knob exhibited a rimose appearance. These ultrastructural characteristics in A. pectospora are similar to those of Z. insidians (Whisler and Travland, 1974) except that the rimose appearance in the terminal knob is replaced in the latter by the fine ridges in the apical, rounded end of the short branches. These similarities led Saikawa and Morikawa (1985) previously to suggest a close relationship between the two species. In the present study, A. pectospora was tested for its ability to capture rotifers instead of nematodes in an aquatic environment, and Z. insidians was tested for its ability to trap nematodes. MATERIALS AND METHODS