bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesized TiO2 nanoparticles and their applications for the treatment of pediatric acute leukemia
Authors: Xiaoshang Gao , Murakonda Gopi Krishna , Jarubula Ramu , Zhao Shushu 
Published: January 2021

Abstract
The current study demonstrates the efficiency of Salvia Spinosa (S. Spinosa) leaf extract in the biofabrication of Titanium dioxide nanoparticles (TiO2 NPs). An easy and green method was used to synthesize TiO2 NPs, which involves the addition of Titanium hydroxide [Ti(OH)2] solution and the leaf extract of S. Spinosa, followed by stirring results in the formation of a light green dispersion of TiO2 NPs. Characterization of the formed TiO2 NPs was performed using the spectroscopic techniques such as FTIR, XRD, EDS, SAED and TEM. The formation of polydisperse TiO2 NPs with a mean particle size of 23 nm was revealed by TEM analysis. The biomolecules that are possibly involved in reducing TiO2 ions are shown in the FTIR spectrum of the S. Spinosa plant leaf extract. Zeta potential results have confirmed the extreme negative charge of 19 mV for the formed TiO2 NPs. The crystalline structure of the fabricated NPs was revealed by the analysis of XRD. In addition, the cytotoxicity results have confirmed that the cytotoxicity against acute lymphoblastic leukemia (Molt-4) cells depends on the dose, further signifying their potential for the advance of new materials and techniques for pediatric leukemia treatment.
From molecular quantum electrodynamics at finite temperatures to nuclear magnetic resonance
Authors: Them Kolja 
Published: January 2021

Abstract
The algebraic reformulation of molecular Quantum Electrodynamics (mQED) at finite temperatures is applied to Nuclear Magnetic Resonance (NMR) in order to provide a foundation for the reconstruction of much more detailed molecular structures, than possible with current methods. Conventional NMR theories are directly related to the effective spin model, which idealizes nuclei as fixed points in a lattice

Z

3

. However, the delocalization of spins due to the thermal energy is more realistically described by the amplitude square of the nuclear wave function ∣Ψ
β
(X)∣2 with

X
∈

R

3
n

, instead of fixed points in

Z

3

. In addition, the phenomenological integration of thermalization only allows an investigation of the molecular structure based on the position of the punctiform center of an NMR signal, but not based on the width and shape of NMR signals. Hence, a lot information on molecular structures remain hidden in experimental NMR data. In this document it is shown how ∣Ψ
β
(X)∣2,

X
∈

R

3
n

can be reconstructed from NMR data. To this end, it is shown how NMR spectra can be calculated directly from mQED at finite temperatures without involving the effective description. The new method connects all data points—the positions, widths, heights and shapes—of NMR signals directly with the molecular structure, which allows more detailed investigations of the underlying system. Furthermore, it is shown that the presented method corrects wrong predictions of the effective spin model. The fundamental problem of performing numerical calculations with the infinite-dimensional radiation field is solved by using a purified representation of a KMS state on a W
*-algebra. It is outlined that the presented method can be applied to any molecular system whose electronic ground state can be calculated using a common quantum chemical method. Therefore, the presented method can replace the effective description which forms the basis for NMR theory since 1950.
Multidimensional analysis of excitonic spectra of monolayers of tungsten disulphide: toward computer-aided identification of structural and environmental perturbations of 2D materials
Authors: Kolesnichenko Pavel V , Zhang Qianhui , Zheng Changxi , Fuhrer Michael S , Davis Jeffrey A 
Published: January 2021

Abstract
Despite 2D materials holding great promise for a broad range of applications, the proliferation of devices and their fulfillment of real-life demands are still far from being realized. Experimentally obtainable samples commonly experience a wide range of perturbations (ripples and wrinkles, point and line defects, grain boundaries, strain field, doping, water intercalation, oxidation, edge reconstructions) significantly deviating the properties from idealistic models. These perturbations, in general, can be entangled or occur in groups with each group forming a complex perturbation making the interpretations of observable physical properties and the disentanglement of simultaneously acting effects a highly non-trivial task even for an experienced researcher. Here we generalise statistical correlation analysis of excitonic spectra of monolayer WS2, acquired by hyperspectral absorption and photoluminescence imaging, to a multidimensional case, and examine multidimensional correlations via unsupervised machine learning algorithms. Using principal component analysis we are able to identify four dominant components that are correlated with tensile strain, disorder induced by adsorption or intercalation of environmental molecules, multi-layer regions and charge doping, respectively. This approach has the potential to determine the local environment of WS2 monolayers or other 2D materials from simple optical measurements, and paves the way toward advanced, machine-aided, characterization of monolayer matter.
Thermal properties of ethylene glycol-carbon based nano-fluids
Authors: Bansal Arti , Sharma Gyan Prakash , Agarwal Ravi , Singh Ramvir 
Published: January 2021

Abstract
We present results of thermal conductivity, thermal diffusivity, and specific heat of Ethylene Glycol (EG)-Carbon nano-fluids obtained using Thermal Constants Analyser (TPS 2200). A two-step method including a magnetic stirrer and an ultrasonic device was used to prepare stable EG-Carbon nano-fluids. Carbon nanoparticles were dispersed slowly in EG with different concentrations of 1 wt%, 2 wt%, 3 wt%, and 4 wt%. Thermal coefficients of the prepared nano-fluids at each concentration were measured at temperatures 10, 20, 30, 40, 50, and 60 °C. The percentage increment in thermal conductivity increases with concentration, as is evident from the observed increments of 20% and 31% for 1 wt% and 4 wt% concentration at 10 ℃, respectively. The highest increase in thermal diffusivity of about 32% was observed when the loading of carbon nanoparticles was increased from 1 wt% to 4 wt% at 10 °C. On the other hand, the same increment in concentration at 10 °C led to a decrease of 15% in specific heat.
First-principles explorations on P8 and N2 assembled nanowire and nanosheet
Authors: Dong Yinan , Wang Shukai , Yu Chunbo , Li Fengyu , Gong Jian , Zhao Jijun 
Published: January 2021

Abstract
‘Bottom-up’ method is a powerful approach to design nanomaterials with desired properties. The bottle neck of being oxidized of phosphorous structures may be conquered by cluster assembling method. Here, we used P8 and N2 as assembling units to construct one-dimensional (1D) nanowire (NW) and two-dimensional (2D) nanosheet (NS), the stability, electronic and magnetic properties of these assembled nanomaterials are investigated using density functional theory (DFT) calculations. The assembled 1D-P8N2 NW and 2D-P8N4 NS are identified to possess good stability, as demonstrated by their high cohesive energies, positive phonon dispersions, and structural integrity through molecular dynamics simulations at 300 and 500 K. Moreover, they also exhibit good anti-oxidization property. The 2D-P8N4 NS is a direct bandgap semiconductor with the HSE06 gap of 2.61 eV, and shows appropriate band-edge aliments and moderate carrier mobility for photocatalyzing water splitting. The 1D-P8N2 NW is an indirect bandgap semiconductor, and Mn doping could convert it into a dilute magnetic semiconductor (DMS) with one Dirac cone in the spin-up channel, while the vdW-type sheet composed of Mn1@1D-P8N2 NWs is a ferromagnetic metal. Our theoretical study is helpful to design stable phosphorus-based nanomaterials with diverse properties and potential applications.
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins
Authors: Mylonas Stelios K , Axenopoulos Apostolos , Daras Petros 
Published: January 2021

Abstract

Motivation
The knowledge of potentially druggable binding sites on proteins is an important preliminary step toward the discovery of novel drugs. The computational prediction of such areas can be boosted by following the recent major advances in the deep learning field and by exploiting the increasing availability of proper data.

Results
In this article, a novel computational method for the prediction of potential binding sites is proposed, called DeepSurf. DeepSurf combines a surface-based representation, where a number of 3D voxelized grids are placed on the protein’s surface, with state-of-the-art deep learning architectures. After being trained on the large database of scPDB, DeepSurf demonstrates superior results on three diverse testing datasets, by surpassing all its main deep learning-based competitors, while attaining competitive performance to a set of traditional non-data-driven approaches.

Availability and implementation
The source code of the method along with trained models are freely available at https://github.com/stemylonas/DeepSurf.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
Authors: Jorquera R , González C , Clausen P T L C , Petersen B , Holmes D S 
Published: January 2021

Abstract
Single-exon coding sequences (CDSs), also known as ‘single-exon genes’ (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases.
Database URL: http://v2.sinex.cl/
Bidirectional endovascular treatment for axillary artery injury secondary to proximal humerus fracture: a case report
Authors: Kanda Daisuke , Imagama Itsumi , Imoto Yutaka , Ohishi Mitsuru 
Published: January 2021

Abstract

Background
Axillary artery injury secondary to proximal humerus fracture is a rare but serious complication. The management of this injury has traditionally involved surgical treatment.

Case summary
A 66-year-old female with gait disturbance slipped and fell off her wheelchair at home. She presented to a local hospital with right shoulder pain and was subsequently urgently transferred to our hospital by helicopter because of suspicion of axillary artery injury. Computed tomography angiography revealed disruption of the right axillary artery. We decided to perform endovascular treatment instead of surgical treatment for axillary artery injury. However, since endovascular treatment via the right femoral artery was impossible, we performed bidirectional (right femoral and right brachial artery approaches) endovascular treatment. We expanded the occluded lesion using a 3.5 mm × 40 mm sized balloon and placed a 5.0 mm × 50 mm stent graft (Gore® Viabahn®) across the lesion. The final subclavian injection confirmed that distal flow to the brachial artery was preserved and that there was no leakage of contrast medium from the axillary artery.

Discussion
We performed endovascular treatment for axillary artery injury secondary to proximal humerus fracture. Although surgical repair is typically performed for this kind of injury, our experience suggests that endovascular treatment might be an option in patients with axillary artery injury.
Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae
Authors: Bendixsen Devin P , Gettle Noah , Gilchrist Ciaran , Zhang Zebin , Stelkens Rike 
Published: January 2021

Abstract
Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer’s yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high-quality long-read genomes of nondomesticated yeast strains isolated from primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new genome assemblies, along with other long-read Saccharomycetes genomes available, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Brewer’s yeast, confirming predictions made from short-read genomic data. Three of these strains (termed the East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early divergence from other S. cerevisiae strains before the larger radiation of the species, and prior to its domestication. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations. The new genomic resources provided here contribute to our understanding of the natural diversity of S. cerevisiae, expand the intraspecific genetic variation found in this heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history.
NATURALLY OCCURRING ENZYME ACTIVITY VARIATION IN DROSOPHILA MELANOGASTER. I. SOURCES OF VARIATION FOR 23 ENZYMES
Authors: Laurie-Ahlberg C C , Wilton A N , Curtsinger J W , Emigh T H 
Published: January 2021

ABSTRACT
The genetic component of variation of enzyme activity levels in Drosophila melanogaster was investigated by using 48 second- and 48 third-chromosome isogenic substitution lines derived from natural populations. The results confirm those of our earlier experiments with the same lines and extend them to a number of additional enzymes. All 23 enzymes show a significant genetic component to the variation in one or both sets of lines and only a small part of this variation is accounted for by variation among the lines in the amount of tissue per fly. The magnitude of line effects is, in most cases, considerably larger than the magnitude of environmental and measurement error effects, and the line effects are approximately continuous in distribution. Variation in the geographic origin and karyotype of the chromosomes generally does not contribute to the line component of variation, but allozymes provide an important source of variation for a few of the enzymes. Many of the enzymes show evidence for variation of activity modifiers that are not linked to the structural locus of the enzyme.
STUDIES ON THE SEX-SPECIFIC LETHALS OF DROSOPHILA MELANOGASTER. IV. GYNANDROMORPH ANALYSIS OF THREE MALE-SPECIFIC LETHALS, mle, msl-2
27 AND mle(3)132
Authors: Uenoyama T , Uchida S , Fukunaga A , Oishi K 
Published: January 2021

ABSTRACT
Mutants at three male-specific lethal loci of Drosophila melanogaster (mle, msl-2 27 and mle(3)132) were examined by gynandromorph analysis. In all cases only a very few gynandromorphs with small X/O patches appeared. Most of these small X/O patches were in the abdomen, and the structures in these X/O regions were reduced in size. These results indicate that the primary effects of these mutants are not on any particular organs or tissues, but rather on individual cells. mle and msl-2 have been shown by Belote and Lucchesi (1980a) to be defective in dosage compensation in X/Y males. We suggest that this dosage-compensation defect results in the expression of Minute-like phenotypes in X/O cells, and hence results in the death of X/O males and flies with large X/O tissue areas.
IDENTIFICATION OF A GENE REGULATING THE TISSUE EXPRESSION OF A PHOSPHOGLUCOMUTASE LOCUS IN RAINBOW TROUT
Authors: Allendorf Fred W , Knudsen Kathy L , Phelps Stevan R 
Published: January 2021

ABSTRACT
Nine percent of the rainbow trout (Salmo gairdneri) from a hatchery source have a greater than 100-fold increase in expression of a phosphoglucomutase (PGM) locus, Pgm1, in the liver but have normal expression of this locus in other tissues. The results of genetic crosses are consistent with a single regulatory gene with additive inheritance being responsible for the differences in the amount of PGM activity in the liver.—The allele responsible for the expression of Pgm1 in the liver is apparently a recent mutation. This is supported by its restricted distribution in rainbow trout and the absence of liver Pgm1 expression in closely related species. This genetic system is valuable for future analysis of the control of gene expression and in determining the relative evolutionary importance of genetic variation at structural and regulatory genes.
ESSENTIAL GENES AND DEFICIENCIES IN THE UNC-22 IV REGION OF CAENORHABDITIS ELEGANS
Authors: Rogalski Teresa M , Moerman Donald G , Baillie David L 
Published: January 2021

ABSTRACT
Five formaldehyde-induced deficiencies that uncover unc-22 IV, a gene affecting muscle structure in the nematode Caenorhabditis elegans were isolated and positioned. The largest deficiency, sDf2, extends in both directions from unc-22 and is approximately 1.0-2.0 map units in length. The other four deficiencies, sDf7, sDf8, sDf9 and sDf10, are all smaller than sDf2 and are located within the region uncovered by this deficiency. Thirty-seven ethyl methanesulfonate-induced lethal and sterile mutations linked to unc-22 were isolated and tested for complementation with sDf2. Nineteen lethal mutations failed to complement sDf2. Sixteen of these were further positioned by recombination mapping and also by deficiency mapping with sDf7, sDf8, sDf9 and sDf10. These sixteen mutations define 11 new essential genes in this region. Eight of the genes lie in a 0.9-map unit interval to the left of unc-22, whereas the three remaining genes lie in a region of about 0.2 map units to the right of unc-22. We believe that two of the essential genes identified in this study, let-56 and let-52, are the adjacent genes on either side of unc-22. The lethal mutations exhibit a wide range of terminal phenotypes: from first stage larva to sterile adult.
IDENTIFICATION OF BRAIN SITES CONTROLLING FEMALE RECEPTIVITY IN MOSAICS OF DROSOPHILA MELANOGASTER
Authors: Tompkins Laurie , Hall Jeffrey C 
Published: January 2021

ABSTRACT
We have identified cells in the brain of Drosophila melanogaster that are required to be of female genotype for receptivity to copulation with males. To do this, we determined experimental conditions in which female flies virtually always copulate, then measured the minimum amount of male courtship that is required to stimulate females to indicate their receptivity to copulation. We then observed gynandromorphs with female genitalia to determine whether the sex mosaics elicited at least the minimum amount of courtship and, if so, whether they copulated. By analyzing these gynandromorphs, in which the genotype of external and internal tissues could be ascertained, we were able to identify a group of cells in the dorsal anterior brain that, when bilaterally female, is necessary and sufficient for receptivity to copulation. This group of cells is anatomically distinct from those that are required to be of male genotype for the performance of courtship behaviors.
GLUCOCORTICOID-INDUCED CLEFT PALATE IN THE MOUSE: TWO MAJOR HISTOCOMPATIBILITY COMPLEX, H-2, LOCI WITH DIFFERENT MECHANISMS
Authors: Bonner Joseph J , Tyan Marvin L 
Published: January 2021

ABSTRACT
Isolated cleft palate is induced in the progeny of pregnant mice that are given glucocorticoids. The incidence varies among inbred strains and with dose and stage of gestation when the drug is given. One chromosomal region responsible for strain-associated differences in sensitivity is the major histocompatibility complex, H-2. H-2a is associated with susceptibility, H-2b with resistance. There appear to be both maternal and embryonic genetic factors affecting the sensitivity to glucocorticoids. In experiments reported here congenic strains of mice with H-2a, H-2d and H-2k haplotypes on a C57BL/10 genomic background were used. This allowed the determination of the effect on sensitivity by two H-2 subregions; the subregions are H-2K to I-E and I-C to H-2D. Methods included dose-response analysis and reciprocal cross analysis using dexamethasone given on day 12 of pregnancy. Results show that each subregion affects the strain's sensitivity to dexamethasone-induced cleft palate. The regression coefficients for B10.A-H-2a (45.4 ± 4.13) were different from those for B10.BR-H-2k (67.2 ± 10.8) and B10.D2-H-2d (70.5 ± 9.74). The estimated mean arcsine% cleft palate at 160 mg/kg was different for each strain: B10.A-H-2a, 53.1 ± 2.19; B10.BR-H-2k, 33.1 ± 2.27; B10.D2-H-2d, 25.0 ± 2.75. Different patterns of change in sensitivity were observed among the reciprocal crosses. In summary, the H-2K to I-E subregion seemed to influence both maternal and embryonic factors, whereas only embryonic factors were influenced by the I-C to H-2D subregion. These data suggest that the mechanisms affecting glucocorticoid sensitivity which are genetically encoded within each H-2 subregion are different, and there is an interaction between the alleles. The mode of interaction can be either complementation or epistasis.
MITOCHONDRIAL FOUR-POINT CROSSES IN ASPERGILLUS NIDULANS: MAPPING OF A SUPPRESSOR OF A MITOCHONDRIALLY INHERITED COLD-SENSITIVE MUTATION
Authors: Waring Richard B , Scazzocchio Claudio 
Published: January 2021

ABSTRACT
Four-point mitochondrial crosses were conducted in heterokaryons of Aspergillus nidulans. The mutations used were (oliA1), conferring resistance to oligomycin, (camA112), conferring resistance to chloramphenicol; (cs-67), conferring cold-sensitivity, and (sumD16), a suppressor of (cs-67). Initially, the crosses were conducted by observing the segregation of extranuclear markers in heterokaryotic sectors emerging from the original point of heterokaryosis. This showed that (camA112), (cs-67) and (sumD16) were linked but were probably all unlinked to (oliA1). Second, four-point crosses were conducted using a double marker selection technique, in which (camA112) and (oliA1) were always set in repulsion and the frequency of the phenotypes produced by the segregation of the mutant and wild-type alleles of (cs-67) and (sumD) were observed in (camA112 oliA1) recombinants. From these results we concluded that (camA112), (cs-67) and (sumD16) were linked and probably mapped in the order given. It was observed that the two nuclear types of conidia from a heterokaryon often had a dissimilar frequency distribution of the segregants of a mitochondrial cross.