Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Correlation for Overall Sherwood Number in Packed Liquid-Liquid Extraction Column

Using plug flow model in conjunction with experimental solute concentration profiles, overall volumetric mass transfer coefficient based on continuous phase (Koca), in a packed liquid-liquid extraction column has been optimized. Number of 12 experiments has been done using standard system of water/acid acetic/toluene in a 6 cm diameter, 120 cm height column. Thorough consideration of influencing parameters we intended to correlate dimensionless parameters in term of overall Sherwood number which has an acceptable average error of about 15.8%. Keywords—Packed column, mass transfer coefficient, solvent extraction, Sherwood number.
Cyanobacterial calcification and its rock‐building potential during 3.5 billion years of Earth history

Microbially mediated calcification can be traced back for at least 2.6 billion years. Although morphological comparison of fossil and recent microbial carbonates suggests that mineralization processes associated with cyanobacteria and their interactions with heterotrophic bacteria have remained similar from the Archaean until today, the metabolic and chemical details remain poorly constrained. Microbial consortia often exhibit an ability to change solution chemistry and control pH at the microscale, passively or actively. This leads to oversaturation of Ca2+ and ions and to the removal of kinetic inhibitors to carbonate precipitation, like sulphate or phosphate. The kinetic barriers of low carbonate ion activity, ion hydration and ion complexing, especially in saline waters, inhibit spontaneous carbonate mineral precipitation from saturated solutions but oxygenic photosynthesis and sulphate reduction by sulphate‐reducing bacteria can overcome these natural barriers. Sulphate in seawater tends to form pairs with Ca2+ and Mg2+ ions. The removal of sulphate reduces complexing, raises carbonate alkalinity, and along with pyrite formation, enhances carbonate precipitation. Cyanobacteria can store Ca2+ and Mg2+ ions in organic envelopes and precipitate carbonates within their sheaths and extracellular polymeric substances, thus, triggering sedimentary carbonate production. We propose that this interplay of cyanobacteria and heterotrophic bacteria has been the major contributor to the carbonate factory for the last 3 billion years of Earth history.
No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines of Saccharomyces cerevisiae

Aneuploidy, the state in which an organism’s genome contains one or more missing or additional chromosomes, often causes widespread genotypic and phenotypic effects. Most often, aneuploidies are deleterious; the most common examples in humans being Down’s syndrome (Trisomy 21) and Turner’s syndrome (monosomy X). However, aneuploidy is surprisingly common in wild yeast populations. In recent years, there has been debate as to whether yeast contain an innate dosage compensation response that operates at the gene, chromosome, or the whole-genome level, or if natural isolates are robust to aneuploidy without such a mechanism. In this study, we tested for differential gene expression in 20 aneuploid and 16 euploid lines of yeast from two previous mutation accumulation experiments, where selection was minimized and therefore aneuploidies arose spontaneously. We found no evidence for whole-chromosome dosage compensation in aneuploid yeast but did find some evidence for attenuation of expression on a gene-by-gene basis. We additionally found that aneuploidy has no effect on the expression of the rest of the genome (i.e. “trans” genes), and that very few mutually exclusive aneuploid lines shared differentially expressed genes. However, we found there was a small set of genes that exhibited a shared expression response in the euploid lines, suggesting an effect of mutation accumulation on gene expression. Our findings contribute to our understanding of aneuploidy in yeast and support the hypothesis that there is no innate dosage compensation mechanism at the whole-chromosome level.
Automatic Creation of a Large-Scale Tempo-Spatial and Semantic Medieval European Information System

In this paper, we automatically create a large tempo-spatial and semantic medieval information system , based on the Regesta Imperii corpus, which contains abstracts of charters issued by medieval European rulers. In order to build this system, we conduct the following two steps: (i) place prediction : we design a bootstrapping method that jointly resolves place names of the locations where a charter was created together with place names mentioned in the charter texts. (ii) semantic linking : we detect places, entities and their interactions with dependency parsing and named entity recognition and aggregate this information together with the place predictions in a single resource. The final resource spans over almost 1000 years of European medieval history. It contains approximately 180,000 place predictions for charter origin places and place predictions for more than one million medieval entities mentioned inside the charter texts, together with their relations. All code is available online under public license: https://github.com/flipz357/regesta-imperii-to-semgis.
Surface plasmon microscopic characterization of external surfaces

Surface plasmon microscopy (SPM) is used, for the first time, to image external samples with a surface relief structure. This is demonstrated in an experimental coupling setup which combines elements of both the Otto and the Kretschmann configuration. The contrast is shown to be generated between areas of different surface plasmon excitation efficiencies. It is shown that periodic surface structures also can be read‐out in Fourier‐space by surface plasmon diffraction. Finally, Fresnel calculations are presented that demonstrate the contrast improvement achievable by immersion SPM using a suitable liquid.
H3K4 Trimethylation Is Required for Postnatal Pancreatic Endocrine Cell Functional Maturation

During pancreas development, endocrine progenitors differentiate into the islet cell subtypes, which undergo further functional maturation in postnatal islet development. In islet β-cells, genes involved in glucose-stimulated insulin secretion are activated, and glucose exposure increases the insulin response as β-cells mature. We investigated the role of H3K4 trimethylation in endocrine cell differentiation and functional maturation by disrupting TrxG complex histone methyltransferase activity in mouse endocrine progenitors. In the embryo, genetic inactivation of TrxG component Dpy30 in NEUROG3+ cells did not affect the number of endocrine progenitors or endocrine cell differentiation. H3K4 trimethylation was progressively lost in postnatal islets, and the mice displayed elevated nonfasting and fasting glycemia as well as impaired glucose tolerance by postnatal day 24. Although postnatal endocrine cell proportions were equivalent to controls, islet RNA sequencing revealed a downregulation of genes involved in glucose-stimulated insulin secretion and an upregulation of immature β-cell genes. Comparison of histone modification enrichment profiles in NEUROG3+ endocrine progenitors and mature islets suggested that genes downregulated by loss of H3K4 trimethylation more frequently acquire active histone modifications during maturation. Taken together, these findings suggest that H3K4 trimethylation is required for the activation of genes involved in the functional maturation of pancreatic islet endocrine cells.
Une modélisation de haut niveau des stratégies d'écriture motrice d'enfants en scolarité primaire : approche bayésienne

L'objectif de cette etude est de decouvrir des strategies d'ecriture motrices des enfants en scolarite primaire en adoptant un modele graphique probabiliste (reseaux bayesiens). Nous representons une strategie d'ecriture par une variable cachee et nous construisons ainsi un modele global hierarchique pour pouvoir lier les strategies locales aux strategies globales et modeliser la dependance probabiliste entre variables et strategies. Ce modele hierarchique, appris a partir des donnees reelles, nous a permis de decouvrir des strategies consistantes et robustes. Ces resultats nous a permis de favoriser une modelisation temporelle et dynamique des strategies d'ecriture motrices independantes de l'âge scolaire.
Circulating ACE2-expressing Exosomes Block SARS-CoV-2 Infection as an Innate Antiviral Mechanism

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19) with innate and adaptive immune response triggered in such patients by viral antigens. Both convalescent plasma and engineered high affinity human monoclonal antibodies have shown therapeutic potential to treat COVID-19. Whether additional antiviral soluble factors exist in peripheral blood remain understudied. Herein, we detected circulating exosomes that express the SARS-CoV-2 viral entry receptor angiotensin-converting enzyme 2 (ACE2) in plasma of both healthy donors and convalescent COVID-19 patients. We demonstrated that exosomal ACE2 competes with cellular ACE2 for neutralization of SARS-CoV-2 infection. ACE2-expressing (ACE2+) exosomes blocked the binding of the viral spike (S) protein RBD to ACE2+ cells in a dose dependent manner, which was 400- to 700-fold more potent than that of vesicle-free recombinant human ACE2 extracellular domain protein (rhACE2). As a consequence, exosomal ACE2 prevented SARS-CoV-2 pseudotype virus tethering and infection of human host cells at a 50-150 fold higher efficacy than rhACE2. A similar antiviral activity of exosomal ACE2 was further demonstrated to block wild-type live SARS-CoV-2 infection. Of note, depletion of ACE2+ exosomes from COVID-19 patient plasma impaired the ability to block SARS-CoV-2 RBD binding to host cells. Our data demonstrate that ACE2+ exosomes can serve as a decoy therapeutic and a possible innate antiviral mechanism to block SARS-CoV-2 infection.
Study of Alkylthiolate Self-Assembled Monolayers on Au(111) using a Semilocal meta-GGA Density Functional

We present a density functional theory study of the structure and stability of self-assembled monolayers (SAMs) of alkylthiolate on Au(111) as a function of the alkyl chain length. The most favorable structure of the SAMs involves an RS−Au−SR complex (S being sulfur, R being an alkyl chain) formed through sandwiching one Au adatom by two alkylthiolates (RSs). Comparing a generalized gradient (GGA-PBE) and a meta-GGA (MGGA-M06-L) exchange-correlation functional we find that only the meta-GGA functional predicts the experimentally observed attractive intermolecular interactions within the SAMs. In particular, the use of M06-L yields an increased stability of the SAMs with increasing alkyl chain length and an increased attractive interaction between RS−Au−SR complexes at shorter distances.
Dietary Monoterpenoids As a New Class of Allosteric Human Aryl Hydrocarbon Receptor Antagonists

Carvones, the constituents of essential oils of dill, caraway, and spearmint, were reported to antagonize the human aryl hydrocarbon receptor (AhR); however, the exact molecular mechanism remains elusive. We show that carvones are non-competitive allosteric antagonists of the AhR that inhibit the induction of AhR target genes in a ligand-selective and cell type-specific manner. Carvones do not displace radiolabeled ligand from binding at the AhR, but they bind allosterically within the bHLH/PAS-A region of the AhR. Carvones did not influence a translocation of ligand-activated AhR into the nucleus. Carvones inhibited the heterodimerization of the AhR with its canonical partner ARNT and subsequent binding of the AhR to the promotor of CYP1A1. Interaction of carvones with potential off-targets, including ARNT and protein kinases, was refuted. This is the first report of a small dietary monoterpenoids as a new class of AhR non-competitive allosteric antagonists with the potential preventive and therapeutic application.
Características produtivas do trigo em função de fontes e doses de nitrogênio

Nitrogen fertilization is an important management practice in grasses and quite complex, due to several factors which influence it, such as climatic conditions, cropping systems and available levels and sources. This study aimed at evaluating the effect of topdressing nitrogen (N) sources and levels on the productive characteristics of wheat ( Triticum aestivum L.) grown after soybean, under no-till system. The experiment was conducted in an Oxisol, in Londrina, Parana State, Brazil. The experimental design was randomized blocks, in a 3x4 factorial scheme, with four replications. As topdressing N sources, urea, urea + urease inhibitor (NBPT) and polymer-coated urea were evaluated, in 2008, and urea, urea + urease inhibitor (NBPT) and ammonium sulfate, in 2009, in four doses (0.0 kg ha -1 , 40.0 kg ha -1 , 80.0 kg ha -1 and 120.0 kg ha -1 of N) applied 20 days after emergence. Plant height, lodging percentage, mass of 1,000 grains, grain yield and hectoliter mass were determined, and results showed that increased topdressing N levels promoted plants lodging, decreasing the mass of 1,000 grains, yield and hectoliter mass. The N sources did not affect the yield of the BRS Pardela cultivar grown after soybean.
Efferent control of hearing sensitivity and protection via inner ear supporting cells

It is well-known that medial olivocochlear (MOC) efferent nerves innervate outer hair cells (OHCs) and inhibit OHC electromotility to control hearing sensitivity. Here, we report that the MOC nerve fibers associated with MOC neurotransmitter acetylcholine (ACh) receptors and presynaptic vesicular acetylcholine transporters (VAChT) also innervated the cochlear supporting cells (SCs). Application of ACh could evoke inward currents in SCs and reduced gap junctions (GJs) between them with long-lasting effect. We further found that uncoupling of GJs between SCs shifted OHC electromotility to the left hyperpolarization direction and enhanced the direct effect of ACh on OHC electromotility. Diminution of this control by deficiency of GJs between SCs compromised the regulation of active cochlear amplification and increased susceptibility to noise. These data suggest that the MOC efferent system has functional innervations with SCs. Such efferent innervation may have an important role in the protection of hearing from noise and slow efferent effect.
Immunoglobulin A antibody composition is sculpted to bind the self gut microbiome

Despite being the most abundantly secreted immunoglobulin isotype, the pattern of reactivity of immunoglobulin A (IgA) antibodies toward each individual’s own gut commensal bacteria still remains elusive. By colonizing germ-free mice with defined commensal bacteria, we found that the binding specificity of bulk fecal and serum IgA toward resident gut bacteria resolves well at the species level and has modest strain-level specificity. IgA hybridomas generated from lamina propria B cells of gnotobiotic mice showed that most IgA clones recognized a single bacterial species, whereas a small portion displayed cross-reactivity. Orally administered hybridoma-produced IgAs still retained bacterial antigen binding capability, implying the potential for a new class of therapeutic antibodies. Species-specific IgAs had a range of strain specificities. Given the distinctive bacterial species and strain composition found in each individual’s gut, our findings suggest the IgA antibody repertoire is shaped uniquely to bind “self” gut bacteria. Description The intestinal IgA antibody repertoire is personalized to bind resident gut bacteria. Custom-tailored gut IgA Much of the secretory immunoglobulin A (IgA) antibody present in the gut lumen is reactive with bacterial antigens, but the degree of specificity this IgA displays across the diverse gut microbiome has not been established. Using germ-free mice recolonized with single bacterial strains or defined consortia of commensal bacteria, Yang et al. investigated the degree of cross-reactivity exhibited by polyclonal fecal and serum IgA or by monoclonal IgA antibodies from IgA hybridoma clones derived from lamina propria B cells. Most IgAs exhibited specificity for the inducing species of gut bacteria, with only a minor fraction of monoclonal IgAs showing broader reactivity. These findings suggest that the bulk secretory IgA repertoire in the gut is personalized to match the community of commensal bacteria residing in the host’s intestine.
TENT4A poly(A) polymerase regulates translesion DNA synthesis and is mutated in endometrial cancer

TENT4A (PAPD7) is a non-canonical poly(A) polymerase, of which little is known. Here we focus on its multilayer regulation of translesion DNA synthesis (TLS), in which DNA lesions are bypassed by error-prone DNA polymerases. We show that TENT4A regulates mRNA stability and/or translation of DNA polymerase η and RAD18 E3 ligase, which guides the polymerase to replication stalling sites, and monoubiquitinates PCNA, thereby enabling recruitment of error-prone DNA polymerases to damaged DNA sites. Remarkably, in addition to the effect on RAD18 mRNA stability via controlling its poly(A) tail, TENT4A indirectly regulates RAD18 via the tumor suppressor CYLD, and via the long non-coding antisense RNA PAXIP1-AS2, which had no known function. Knocking down the expression of TENT4A or CYLD, or overexpression of PAXIP1-AS2 led each to reduced amounts of the RAD18 protein and DNA polymerase η, leading to reduced TLS, highlighting PAXIP1-AS2 as a new TLS regulator. Bioinformatics analysis revealed that TLS error-prone DNA polymerase genes and their TENT4A-related regulators are frequently mutated in endometrial cancer genomes, suggesting that TLS is dysregulated in this cancer.
Tissue heterogeneity is prevalent in gene expression studies

Background Lack of reproducibility in gene expression studies has recently attracted much attention in and beyond the biomedical research community. Previous efforts have identified many underlying factors, such as batch effects and incorrect sample annotations. Recently, tissue heterogeneity, a consequence of unintended profiling of cells of other origins than the tissue of interest, was proposed as a source of variance that exacerbates irreproducibility and is commonly ignored. Results Here, we systematically analyzed 2,692 publicly available gene expression datasets including 78,332 samples for tissue heterogeneity. We found a prevalence of tissue heterogeneity in gene expression data that affects on average 5-15% of the samples, depending on the tissue type. We distinguish cases of severe heterogeneity, which may be caused by mistakes in annotation or sample handling, from cases of moderate heterogeneity, which are more likely caused by tissue infiltration or sample contamination. Conclusions Tissue heterogeneity is a widespread issue in publicly available gene expression datasets and thus an important source of variance that should not be ignored. We advocate the application of quality control methods such as BioQC to detect tissue heterogeneity prior to mining or analysing gene expression data.
The role of replication clamp-loader protein HolC of Escherichia coli in overcoming replication / transcription conflicts

In Escherichia coli, DNA replication is catalyzed by an assembly of proteins, the DNA polymerase III holoenzyme. This complex includes the polymerase and proofreading subunits as well as the processivity clamp and clamp loader complex. The holC gene encodes an accessory protein (known as x) to the core clamp loader complex and is the only protein of the holoenzyme that binds to single-strand DNA binding protein, SSB. HolC is not essential for viability although mutants show growth impairment, genetic instability and sensitivity to DNA damaging agents. In this study, to elucidate the role of HolC in replication, we isolate spontaneous suppressor mutants in a holCΔ strain and identify these by whole genome sequencing. Some suppressors are alleles of RNA polymerase, suggesting that transcription is problematic for holC mutant strains or sspA, stringent starvation protein. Using a conditional holC plasmid, we examine factors affecting transcription elongation and termination for synergistic or suppressive effects on holC mutant phenotypes. Alleles of RpoA (α), RpoB (β) and RpoC (β’) RNA polymerase holoenzyme can partially suppress loss of HolC. In contrast, mutations in transcription factors DksA and NusA enhanced the inviability of holC mutants. Mfd had no effect nor did elongation factors GreA and GreB. HolC mutants showed enhanced sensitivity to bicyclomycin, a specific inhibitor of Rho-dependent termination. Bicyclomycin also reverses suppression of holC by rpoA rpoC and sspA.These results are consistent with the hypothesis that transcription complexes block replication in holC mutants and Rho-dependent transcriptional termination and DksA function are particularly important to sustain viability and chromosome integrity. IMPORTANCE Transcription elongation complexes present an impediment to DNA replication. We provide evidence that one component of the replication clamp loader complex, HolC, of E. coli is required to overcome these blocks. This genetic study of transcription factor effects on holC growth defects implicates Rho-dependent transcriptional termination and DksA function as critical. It also implicates, for the first time, a role of SspA, stringent starvation protein, in avoidance or tolerance of replication/replication conflicts. We speculate that HolC helps resolve codirectional collisions between replication and transcription complexes, which become toxic in HolC’s absence.
Optimization of femtosecond laser plasma Ka sources

Die Eigenschaften der Ka-Rontgenemission von laserproduzierten Plasmen wurden mit Hilfe eines numerischen Simulationsmodells und der zweidimensionalen monochromatischen Abbildung der Emission untersucht. Mit Daten aus dem Simulationsmodell wurde ein Skalierungsgesetz fur die optimale Laserintensitat zur Erzeugung von Ka-Strahlung abgeleitet. Fur hohe Laserintensitaten zeigt die gemessene raumliche Struktur der Ka-Quelle Abweichungen vom Simulationsmodell, die qualitativ durch selbstinduzierte Felder erklart werden konnen. Die berechneten Rontgenpulsdauern stimmen mit denen aus Pump-Probe-Experimenten uberein.
In Vitro Capacitation of Ram Spermatozoa

Epididymus were collected from Al-Ramadi Slaughter house during the periods from September 2002 to march 2003. The samples were transported to the Laboratory with normal saline at a temp of 33-35c within 30 minutes. Semen were collected from the tail of epididymus by aspiration with 18 gauge needle on 3ml disposable suring containing 1-2 ml TALP media. The collected media together with spermatozoa were put in a Petri dish and incubated in Co2 incubator at 35 c, 90% Humidity for 4-6 h. Spermatozoa evaluated for their maturation (The distal Protoplasmic droplet). Matured Spermatozoa were washed with buffer Solution. Three times with Centrifugation. Then 0.5 ml of spermatozoa pluse 9.5 ml of TALP media with 10 mg/ml heparin, Centrifuged, and then 0.5 ml from the bottom spermatozoa incubated in Co2 incubator at 35c with 45 angle. Head to Head agglutination of Spermatozoa was considered the Criteriia of sperm Capacitation. The results showed that the procedures give a best result for sperm maturation and capacitation in vitro. It was concluded that a possibility of sperm maturation and capacition taken from cauda epididymus of ram from slaughter house sources. ایربتخم شبكلا نمایح فییكت