jimnoneill/paper-to-field-training huggingface dataset:
<i>CD79B </i>mutations in primary vitreoretinal lymphoma: Diagnostic and prognostic potential

Abstract Objective Primary vitreoretinal lymphoma (PVRL) is a rare type of lymphoma wherein the lesions are limited to the eyes. PVRL is difficult to diagnose because of the challenges related to obtaining sufficient samples for biopsy. Moreover, PVRL has poor outcomes and often leads to the development of central nervous system (CNS) lesions during its course. Two studies recently reported that approximately 70%‐80% of patients with vitreoretinal lymphoma have MYD88 L265P , which is frequently mutated in primary CNS lymphoma (PCNSL). PCNSL is closely associated with PVRL. The mutation of CD79B Y196 has been also frequently detected in PCNSL. Thus, we examined the mutation in PVRL to clarify its diagnostic and prognostic potential. Method By using direct sequencing and allele‐specific polymerase chain reaction, we examined the mutation of CD79B Y196 and MYD88 L265P in the DNA extracted from the vitreous fluid of 17 patients with PVRL upon diagnosis. We also retrospectively analyzed their prognostic potential for PVRL. Results Among the included patients, six patients (35%) were found with CD79B Y196 mutations. Twelve (71%) patients were positive for MYD88 L265P , and six samples from patients with benign uveitis were negative for both mutations. Interestingly, six patients with CD79B Y196 mutations developed CNS diseases significantly earlier (16.5 months) than 11 patients with CD79B WT (67 months; P = 0.0135). Conclusion Detecting CD79B Y196 in vitreous DNA may contribute to the confirmation of the diagnosis and may have a prognostic potential for patients with PVRL.

Topic: CNS Lymphoma Diagnosis and Treatment
Subfield: Neurology
Field: Medicine
Domain: Health Sciences
Lensless object scanning holography for diffuse objects

Recently proposed, Lensless Object Scanning Holography (LOSH) is a fully lensless method, capable of improving image quality in digital Fourier holography applied to reflective objects, and involving a very simplified experimental setup. LOSH is based on the recording and digital post-processing of a set of digital lensless Fourier transform holograms which finally results in a synthetic image with improved resolution, field of view (FOV), signal-to-noise ratio (SNR), and depth of field (DOF). In this paper, LOSH is expanded to the case of diffuse-based objects. Now, the speckle can affect the resolution and it will not be a function of only the size of the aperture. The fact of increasing the aperture can produce the decrease of the size of the speckle. Moreover, there is an overlapping of speckles of the successive images. Different kinds of digital processing can be applied to obtain the final synthetic image. Among them, partial coherent processing, arising from the incoherent sum of several sets of images coherently added, provides the best improvement in the resolution and also in the SNR due to partial averaging of the speckles. Experimental results for a diffuse object are presented for different kinds of digital processing.

Topic: Digital Holography and Microscopy
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences
Deuteration Effect of Ferroelectricity and Permittivity on Homochiral Zinc Coordination Compound

Hydrothermal [2+3] cycloaddition reactions of N-4'-caynobenzylcinchonidine bromide (CBCBr) with NaN3 in the presence of ZnBr2 offer a novel Zn dimer (CBC−N4)2ZnBr2(N3)2(X2O), X = H for 1 and D for 2) in which the reactant Br- and N3- take part in the coordination to Zn. The measurements of ferroelectricity and permittivity of 1 and 2 show that there exists a large deuterated effect both in ferroelectric behavior (40% increase) and in dielectric constant (2.75 times increase), which is unprecedented in metal coordination compounds.

Topic: Magnetism in coordination complexes
Subfield: Electronic, Optical and Magnetic Materials
Field: Materials Science
Domain: Physical Sciences
Pasteurella multocida produces a protein with homology to the P6 outer membrane protein of Haemophilus influenzae

An antibody specific for a 16-kDa outer membrane protein of a rabbit strain of Pasteurella multocida was used to probe representatives of all 16 somatic serotypes of P. multocida, as well as the vaccine strains CU and M9, and all were shown to express the protein. The gene encoding this protein was cloned and sequenced and found to have extensive sequence homology with the gene encoding the P6 protein of Haemophilus influenzae. The protein in P. multocida has been designated P6-like. The gene encoding the P6-like protein was used to probe members of the family Pasteurellaceae and other gram-negative bacteria. Representatives of all 16 somatic serotypes (as well as the vaccine strains CU and M9) of P. multocida hybridized with the P6-like gene under conditions of high stringency. The DNA from H. influenzae hybridized weakly with the P6-like gene under these conditions, but Pasteurella haemolytica (representatives of A and T biotypes), Bordetella bronchiseptica, B. avium, Actinobacillus suis, A. suis-like, A. lignieresii, A. ureae, A. rossii, A. pleuropneumoniae, A. equuli, and various members of the family Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Salmonella typhimurium) did not hybridize detectably. Under conditions of lower stringency, the P6-like gene also hybridized strongly with DNA from P. multocida, H. influenzae, and A. rossii but weakly with DNA from P. haemolytica and members of the genus Actinobacillus. These results suggest that the P6-like protein of P. multocida might be useful as an immunizing product to protect poultry from avian cholera. This suggestion stems from (i) our finding that the P6-like protein in P. multocida is widely distributed among all the somatic serotypes and (ii) the previous work of others demonstrating that the P6 protein of H. influenzae elicits a protective immune response in animal models of human disease.

Topic: Microbial infections and disease research
Subfield: Microbiology
Field: Immunology and Microbiology
Domain: Life Sciences
nanostructured hydrogen gas sensors

In this paper, we discuss the progress of nitride and oxide semiconductor nanostructures for hydrogen gas sensing. The use of catalyst metal coatings on GaN, InN and ZnO nanowires is found to greatly enhance the detection sensitivity. Pt- and Pd-coated GaN nanowires biased at small voltages show large changes in currents upon exposure to H2 gas at concentrations in the ppm range. Improvements in growth techniques for InN nanostructures have produced nanobelts and nanorods capable of hydrogen detection down to 20 ppm after catalyst coating. Functionalized ZnO nanorods were also investigated for hydrogen detection, but did not generate a relative response as high as that for the nitride-based sensors. All sensors tested exhibited no response at room temperature upon exposure to various other gases including O2, C2H5, N2O and CO2. The high surface-to-volume ratio of nanowires and the ability to use simple contact fabrication schemes make them attractive for hydrogen sensing applications. (Some figures in this article are in colour only in the electronic version)

Topic: Gas Sensing Nanomaterials and Sensors
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Peer Review #2 of "Effects of poly (ADP-ribose) polymerase-1 (PARP-1) inhibition on sulfur mustard-induced cutaneous injuries in vitro and in vivo (v0.2)"

Early studies with first-generation poly (ADP-ribose) polymerase (PARP) inhibitors have already indicated some promising therapeutic potential in sulfur mustard (SM) injury.The available novel and more potential PARP inhibitors, which are undergoing clinical trials as drugs for cancer treatment, bring it back to the centre of interest.However, the role of PARP-1 in SM-induced injury is not fully understood.In this study, we selected a high potent specific PARP inhibitor ABT-888 as example to investigate the effect of PARP inhibitor in SM injury.The results showed that in mouse ear vesicant model (MEVM) and HaCaT cell model, PARP inhibitor ABT-888 could reduce the cell damage induced by severe SM injury.ABT-888 significantly reduced SM induced edema and epidermal necrosis in MEVM.In HaCaT cell model, ABT-888 could reduce SM-induced NAD + /ATP depletion and apoptosis/necrosis.Then, we study the mechanism of PARP-1 in SM injury by knockdown of PARP-1 in HaCaT cells.Knockdown of PARP-1 protected cell viability and downregulated the apoptosis checkpoints, including p-JNK, p-P53, Caspase 9, Caspase 8, c-PARP andCaspase 3 following SM-induced injury.Furthermore, the activation of AKT can inhibit autophagy via the regulation of mTOR.Our results showed that SM exposure could significantly inhibit the activation of Akt/mTOR pathway.Knockdown of PARP-1 reversed the SM-induced suppression of the Akt/mTOR pathway.In summary, the results of our study indicated that the protective effects of downregulation of PARP-1 in SM injury may be due to the regulation of apoptosis, necrosis, energy crisis and autophagy.However, it should be noticed that PARP inhibitor ABT-888 further enhanced the phosphorylation of H2AX (S139) after SM exposure, which indicated that we should be very careful in the application of PARP inhibitors in SM injury treatment because of the enhancement of DNA damage.

Topic: Insect and Pesticide Research
Subfield: Insect Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Different regions of aminoacyl-tRNA regulate the function of elongation factor Tu.

In this work we show that intact aminoacyl-tRNA (aa-tRNA) and its 3' half-molecule, but not its 3' C-C-A-aa fragment, require selective ionic conditions for stimulating the mRNA-independent GTPase of elongation factor Tu (EF-Tu) in the presence of ribosomes.l Stimulation by aa-tRNA and its 3' half-molecule is only observed at 20 and 30 mM Mg2+ and not at 10 mM, where they exert inhibitory activity; by contrast, C-C-A-aa enhances the GTPase activity at all three of these Mg2+ concentrations. Ammonium ion is needed for stimulation by C-C-A-aa, whereas it inhibits the stimulation by aa-tRNA and its 3' half-molecule. The concentration of aminoacylated fragments needed for half-maximum stimulation follows this order: A-Val much greater than C-A-Val greater than C-C-A-Val much greater than 3' Val-tRNA1Val half-molecule greater than Val-tRNA1Val. The extent of maximum stimulation of the EF-Tu GTPase in the presence of ribosomes varies moderately depending on the aa-tRNA species; a clear dependence on the nature of the aminoacyl side chain is observed in the effects of their respective C-C-A-aa fragments tested (C-C-A-Arg, C-C-A-Val, C-C-A-Phe, C-C-A-Met, C-C-A-Lys). In the absence of ribosomes and at low [Mg2+], the one-round GTP hydrolysis by EF-Tu is enhanced by C-C-A-aa fragments, whereas it is inhibited by the corresponding aa-tRNAs. Our results suggest that besides the 3' aminoacylated extremity another region(s) of the aa-tRNA molecule controls the GTPase of EF-Tu. The "unspecific" stimulation by C-C-A-aa and the "specific," aa-tRNA-like effect of the 3' aa-tRNA half-molecule point to the importance of the T chi C loop and stem, as well as of the adjacent regions for the regulation of this function.

Topic: RNA and protein synthesis mechanisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Figure S2 from Aspirin Inhibits Cancer Metastasis and Angiogenesis via Targeting Heparanase

&lt;p&gt;supplementaty Figure S2 shows the inhibitory effect of aspirin and salicylic acid on degradation of heparan sulfate by heparanase&lt;/p&gt;

Topic: Proteoglycans and glycosaminoglycans research
Subfield: Cell Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Evaluation of antioxidant properties in pickled lime and watermelon peels during storage / Zamlizawati Mohd Zain

Lime and watermelon peel were analyzed for antioxidant activity measured in ethanol extract. Total Phenolic Content used the Gallic acid as the standard, Total Flavanoid Content that used quercetin as standard, 1,1- diphenyl-2-picrylhydrazyl used the Ascorbic Acid as the standard and Ferric Reducing Ability of Plasma used the Trolox as the standard which method were used for determining antioxidant properties. The procedure gave results of single pickle where lime peel gave higher antioxidant compared to the watermelon peel. While, storage pickle gave result of decreasing antioxidant activity, where weekl &gt; week2 &gt; week3. Then the result of mixed pickled (cooked and fresh pickle), results that the cooked have higher antioxidant activity. Results from formulation, (80 LP: 20 WR &gt;60 LP: 40 WR &gt; 30 LP: 70 WR) showing that the first formulation (80LP: 20WR) have higher antioxidant activity.

Topic: Insect behavior and control techniques
Subfield: Insect Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Effect of Pantothenic Acid Deficiency on Lipid Metabolism in the Yeast

To investigate the influence of pantothenic acid deficiency on mitochondria, Saccharomyces cerevisiae, a pantothenate requiring strain isolate from a commercial baker's yeast was cultured with a pantothenate sufficient (200μg/liter) and a deficient (10μg/liter) medium. These microorganisms were observed morphologically with the electron microscope and analyzed for the lipid composition. And it was recognized that in pantothenate sufficient cells the existence of mitochondria was clear enough, but in the deficient cells the membrane structure of mitochondria was not proved. However, when pantothenate was sufficiently added to the cells in the deficient medium at the exponential phase the formation of mitochondria was detected after 18 hours as in the sufficient cells.In the pantothenate deficient cells, the formation of lipids was markedly inhibited, and phospholipid constituted was almost 85% of the total lipid. And the amount of 32P incorporated into the deficient cells was two times that in the sufficient cells, but the ratio of the count of phospholipid-32P relative to the total was somewhat lower than that of the sufficient cells.In the pantothenate sufficient yeast, the principal fatty acid in total lipid, neutral fat and phospholipid was found to be palmitoleic acid followed by oleic acid regardless of the kind of lipid. In contract, in the deficient cells, oleic acid was the principal component and palmitoleic acid followed it. These results may suggest that (I) pantothenate deficiency affects the membrane formation through the disturbance of lipid metabolism and (II) the organism plays an economical control on the fatty acid synthesis in the deficient condition.

Topic: Neurological diseases and metabolism
Subfield: Neurology
Field: Neuroscience
Domain: Life Sciences
Immunohistochemical identification of serotonin and noradrenalin containing structures within the nerve plexuses of rat ileum.

The distribution of 5-hydroxytryptamine (= serotonin = 5-HT) and noradrenalin (NA) in the enteric plexuses of the rat ileum was studied using immunocytochemical techniques. 5-HT-like immunoreactive fibers were observed only in the myenteric plexus, surrounding the ganglionic cells, which are all unreactive. NA-like immunoreactive fibers were present in all layers of the ileum: in the myenteric plexus, they were localized in the nodes, forming a network all round the neuronal perikarya; in the Meissner plexus, positive axons were arranged in a delicate network; submucosal blood vessels were often provided by NA-immunopositive nerve plexus. In the inner circular muscle layer the immunoreactive NA-positive fibers run within nerve bundles mainly parallel with the smooth muscle cells. The 5-HT immunoreactive material was depleted by treatment with reserpine; depletion of NA by 6-hydroxy-dopamine was also observed; on the contrary, no depletion of 5-HT by 5,7-dihydroxytryptamine was obtained. To confirm the validity of these results, specific antibodies to tyrosine hydroxylase (TH) and aromatic 1-aminoacid-decarboxylase (AADC), two enzymes involved in the synthesis of catecholamines, were used. In conclusion these experiments indicate that 5-HT is present, probably as a transmitter, in certain fibres of the rat myenteric plexus, distributed in a way similar to that of NA-containing fibers. However, at variance with NA fibers, 5-HT fibers are not present in other regions of the intestine wall.

Topic: Diet and metabolism studies
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
Analisis Pengaruh Bantuan Pangan Non Tunai dan Program Keluarga Harapan Terhadap Kemiskinan di Kota Mojokerto Tahun 2019-2021

Poverty is a condition when a person or a group has no choice to fulfill their essential privileges to maintain and maintain a noble life. The poverty rate in Mojokerto City has increased significantly over the last three years. Compared to the surrounding districts/cities, the increase in poverty is not as severe as in Mojokerto City. This study aims to analyze how PKH and BPNT influence poverty in Mojokerto City in 2019-2021. The type of data used in this research is secondary data, then for the approach that is quantitative, with the type of research descriptive analysis, using multiple linear regression through data processing in SPSS 22. The study found that PKH had a negative and significant impact on poverty, while BPNT had a positive and significant impact on poverty.

Topic: Food Security and Socioeconomic Dynamics
Subfield: General Agricultural and Biological Sciences
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Summary on marine biological diversity

This Part of the State of the Coast Report presents an Assessment of Marine Biological Diversity and Habitats in the Western Indian Ocean. Its scope is thus wide and the various chapters deal with the multiple ecosystems found in the region, as well as the full diversity of biota they support. Some of the latter are found in a number of environments at different stages of their life cycle and thus warrant inclusion in a number of chapters; the best example is that of turtles which nest on beaches, feed on reefs, seagrass beds or in pelagic waters, and traverse the open ocean in their movements. For completion, the Part also includes a chapter on human dependence on the region’s biodiversity.

Topic: Identification and Quantification in Food
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Corporate Social Responsibility And Tax Avoidance: Evidence From Korean Firms

This study examines the relationship between corporate socially responsible (CSR) activities and tax avoidance using residual book-tax differences (BTD), year residual BTD and total BTD. Using a sample of 1,148 publicly listed Korean firms on Korean Stock Exchange (KSE) covering periods between 2004 and 2009 it finds that the firms with higher CSR activities are less likely to avoid taxes regardless which proxy of tax avoidance is used. This finding is confirmed with two stage least square (2SLS) method after accounting for endogeneity of CSR. It also tests how seven different CSR activities affect tax avoidance, and finds that social services, satisfaction of employees and contributions to economic development are negatively related to tax avoidance. Overall, the empirical results of this paper support the previous studies arguing the negative relationship between tax avoidance and CSR.

Topic: Corporate Taxation and Avoidance
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
Relation between growth dynamics and diffusional limitations in<i>Saccharomyces cerevisiae</i>cells growing as entrapped in an insolubilised gelatin gel

Flow-cytometric analysis was employed to investigate growth dynamics of a yeast cell population immobilised in an insolubilised gelatin gel by means of the quantitative determination of the average protein content per cell. This analysis was carried out on both the immobilised cell population considered as a whole and the subpopulations colonising the gelatin matrix at different depths. The results show that growth of the gelatin-immobilised yeast population was affected by the existence of a gradient of nutrient concentrations through the matrix and are in agreement with the unsteady-state diffusion model employed for the description of glucose transfer in the gel.

Topic: Polysaccharides Composition and Applications
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
How Visualising Emotions Affects Interpersonal Trust and Task Collaboration in a Shared Virtual Space

Emotion is dynamic. Changes in emotion can be hard to process during face-to-face interaction, yet transferring them into a shared virtual space becomes more challenging. This research first explores nine visual representations to amplify emotions in a virtual space, leading to a bi-directional emotion-sharing system (FeelMoji i/o). The second study investigates the effect of explicit emotion-sharing in interpersonal trust and task collaboration through three conditions - verbal only, verbal+positive visual, and verbal+honest visual using FeelMoji through the proposal of a framework of four factors (usability, integrity, behaviour, and collaboration). The results indicate that FeelMoji yields frequent emotion consensus as task milestones and positive interdependent behaviours between collaborators, which help develop conversations, affirm decision-making, and build familiarity and trust between strangers. Moreover, we discuss how our study can inspire future investigation in human-AI agent behaviours and large-scale multi-user virtual environments.

Topic: Virtual Reality Applications and Impacts
Subfield: Human-Computer Interaction
Field: Computer Science
Domain: Physical Sciences
What palatalized consonants can tell us about theories of loanword adaptation

Phonology- and perception-based theories of loanword adaptation clash over two different assumptions: what language background the adapter has and what cognitive component handles adaptation. Phonology-based theories argue that borrowers know both the source and borrowing language and that the phonology determines output forms; perception-based accounts argue that the borrower does not know the source language and that the phonetic decoder guides adaptation. Since there is no reason to believe that either population of borrowers cannot adapt words, a production experiment was carried out to test both populations/approaches. Four monolingual English and three bilingual English-Russian speakers were played currently unborrowed Russian words containing palatalized consonants and asked to repeat them aloud in an American English accent. Since palatalized velar and coronal stops are often articulated with some degree of affrication and monolinguals are unaware of this, it was predicted that they would sometimes adapt said consonants as affricates (tju &amp;gt; t∫u). However, since bilinguals are familiar with the co-articulatory affrication, they were not predicted to adapt palatalized stops as affricates (tju &amp;gt; tu). The results corroborated the hypothesis in that bilinguals never affricated while monolinguals affricated a tenth of palatalized stops—demonstrating that both theories make the correct predictions for their respective populations.

Topic: Phonetics and Phonology Research
Subfield: Experimental and Cognitive Psychology
Field: Psychology
Domain: Social Sciences