Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell adhesion proteins in the cerebrospinal fluid of neonates prenatally exposed to Zika virus: A case–control study

To compare cell adhesion molecules levels in cerebrospinal fluid (CSF) between Zika virus (ZIKV)‐exposed neonates with/without microcephaly (cases) and controls, 16 neonates (cases), 8 (50%) with and 8 (50%) without microcephaly, who underwent lumbar puncture (LP) during the ZIKV epidemic (2015–2016) were included. All mothers reported ZIKV clinical symptoms during gestation, all neonates presented with congenital infection findings, and other congenital infections were ruled out. Fourteen control neonates underwent LP in the same laboratory (2017–2018). Five cell adhesion proteins were measured in the CSF using mass spectrometry. Neurexin‐1 (3.50 [2.00–4.00] vs. 7.5 [5.00–10.25], P = 0.001), neurexin‐3 (0.00 [0.00–0.00] vs. 3.00 [1.50–4.00], P = 0.001) and neural cell adhesion molecule 2 (NCAM2) (0.00 [0.00–0.75] vs. 1.00 [1.00–2.00], P = 0.001) were significantly lower in microcephalic and non‐microcephalic cases than in controls. When these two sub‐groups of prenatally ZIKA‐exposed children were compared to controls separately, the same results were found. When cases with and without microcephaly were compared, no difference was found. Neurexin‐3 (18.8% vs. 78.6%, P = 0.001) and NCAM2 (25.0% vs. 85.7%, P = 0.001) were less frequently found among the cases. A positive correlation was found between cephalic perimeter and levels of these two proteins. Neurexin‐2 and neurexin‐2b presented no significant differences. Levels of three cell adhesion proteins were significantly lower in CSF of neonates exposed to ZIKV before birth than in controls, irrespective of presence of congenital microcephaly. Moreover, the smaller the cephalic perimeter, the lower CSF cell adhesion protein levels. These findings suggest that low CSF levels of neurexin‐1, neurexin‐3 and NCAM2 may reflect the effects of ZIKV on foetal brain development.
A FAST REDUCTION METHOD OF SURVEY DATA IN RADIO ASTRONOMY

We present a fast reduction method of survey data obtained using a single-dish radio telescope. Along with a brief review of classical method, a new method of identification and elimination of negative and positive bad channels are introduced using cloud identification code and several IRAF (Image Reduction and Analysis Facility) tasks relating statistics. Removing of several ripple patterns using Fourier Transform is also discussed. It is found that BACKGROUND task within IRAF is very efficient for fitting and subtraction of base-line with varying functions. Cloud identification method along with the possibility of its application for analysis of cloud structure is described, and future data reduction method is discussed.
Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia

Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling. ABSTRACT Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.
Biological Control of Melon Continuous Cropping Obstacles: Weakening the Negative Effects of the Vicious Cycle in Continuous Cropping Soil

The soil environment, crop growth and fruit quality of melons are negatively affected by long-term continuous cropping. It is important to study the mechanism of continuous cropping obstacles and their biological control. ABSTRACT The continuous cropping obstacles of melons have become increasingly serious in recent years. To investigate this, we explored the effects and mechanisms of Bacillus subtilis C3 in control of the continuous cropping obstacles of melon. We provide a novel interaction model of the occurrence factors of continuous cropping obstacles. The dominant pathogen isolated from melon soil was Fusarium. Their hyphae were used as food to cultivate root-knot nematodes. The main phenolic acids in melon soil promoted the growth of Fusarium and indirectly increased the number of root-knot nematodes, but they also had direct toxic effects on melon root-knot nematodes. The simultaneous inoculation of the three had the strongest inhibitory effect on melon seedlings, while the inhibitory effect of paired inoculation was weaker than that of single inoculation. Therefore, the three balance each other, forming a vicious cycle. Bacillus subtilis C3 weakened the negative effects of this cycle on melon by eliminating phenolic acids and inhibiting the growth of Fusarium and root-knot nematodes. Simultaneously, they also alleviated the continuous cropping obstacles of melon by improving the composition and structure of the rhizosphere microbial community. Our results might be useful for the effective control of the continuous cropping obstacles of melon. IMPORTANCE The soil environment, crop growth and fruit quality of melons are negatively affected by long-term continuous cropping. It is important to study the mechanism of continuous cropping obstacles and their biological control. In this study, we propose a novel interaction model of the occurrence factors of continuous cropping obstacles. The dominant phenolic acids, pathogenic fungi, and root-knot nematodes from melon soil balance each other, forming a vicious cycle. Bacillus subtilis C3 weakened the negative effects of this cycle on melon by eliminating phenolic acids and inhibiting the growth of Fusarium and root-knot nematodes. In addition, C3 also improved the composition and structure of the melon rhizosphere microbial community. These results advance the study of the occurrence mechanism of continuous cropping obstacles and demonstrate an efficient and environmentally friendly biological control scheme.
Singularities of Nonconfluent Hypergeometric Functions in Several Variables

The paper deals with singularities of nonconfluent hypergeometric functions in several variables. Typically such a function is a multi-valued analytic function with singularities along an algebraic hypersurface. We describe such hypersurfaces in terms of amoebas and the Newton polytopes of their defining polynomials. In particular, we show that all A-discriminantal hypersurfaces (in the sense of Gelfand, Kapranov and Zelevinsky) have solid amoebas, that is, amoebas with the minimal number of complement components.
Texture transformer super-resolution for low-dose computed tomography

Computed tomography (CT) is widely used to diagnose many diseases. Low-dose CT has been actively pursued to lower the ionizing radiation risk. A relatively smoother kernel is typically used in low-dose CT to suppress image noise, which may sacrifice spatial resolution. In this work, we propose a texture transformer network to simultaneously reduce image noise and improve spatial resolution in CT images. This network, referred to as Texture Transformer for Super Resolution (TTSR), is a reference-based deep-learning image super-resolution method built upon a generative adversarial network (GAN). The noisy low-resolution CT (LRCT) image and the routine-dose high-resolution (HRCT) image are severed as the query and key in a transformer, respectively. Image translation is optimized through deep neural network (DNN) texture extraction, correlation embedding, and attention-based texture transfer and synthesis to achieve joint feature learning between LRCT and HRCT images for super-resolution CT (SRCT) images. To evaluate SRCT performance, we use the data from both simulations of the XCAT phantom program and the real patient data. Peak signal-to-noise ratio (PSNR), structural similarity index measure (SSIM), and feature similarity (FSIM) index are used as quantitative metrics. For comparison of SRCT performance, the cubic spline interpolation, SRGAN (a GAN super-resolution with an additional content loss), and GAN-CIRCLE (a GAN super-resolution with cycle consistency) were used. Compared to the other two methods, TTSR can restore more details in SRCT images and achieve better PSNR, SSIM, and FSIM for both simulation and real-patient data. In addition, we show that TTSR can yield better image quality and demand much less computation time than high-resolution low-dose CT images denoised by block-matching and 3D filtering (BM3D) and GAN-CIRCLE. In summary, the proposed TTSR method based on texture transformer and attention mechanism provides an effective and efficient tool to improve spatial resolution and suppress noise of low-dose CT images.
Exposure to nitrosatable drugs during pregnancy and childhood cancer: A matched case–control study in Denmark, 1996–2016

Nitrosatable drugs can be synthesized to N‐nitroso compounds in human stomach. In a pregnant woman, N‐nitroso compounds can be translocated to the fetus through the placenta. Maternal exposure of nitrosatable compounds during pregnancy has been associated with childhood brain tumors and leukemia. However, few studies have investigated an association between nitrosatable drug exposure during pregnancy and childhood cancer. We examined if maternal prescriptions of nitrosatable drugs received during pregnancy are associated with childhood cancer.
First Molecular Detection of Pneumocystis spp. in the Golden Jackal (Canis aureus)

Abstract: Forty-six golden jackals (Canis aureus) were collected between November 2020 and February 2021 in five counties of Serbia. Lung samples were screened for the presence of Pneumocystis DNA by pan-Pneumocystis PCR on the mtLSU rRNA gene obtaining PCR products of 370 bp in length. Pneumocystis DNA was detected in the lungs from 6/46 (13.04%) golden jackals. Four were females and two were males; four were classified as adults and two as subadults. Positive samples were confirmed in 4/5 investigated counties. No gross pathologic lung lesions were observed in this study. The sequences of Pneumocystis spp. from golden jackals were identical to one another and showed the highest similarity with Pneumocystis spp. sequences of dogs (98% nucleotide identity). The genetic variation was comparable to Pneumocystis spp. of raccoon dogs (95–97% nucleotide identity), red foxes (91–95% nucleotide identity), ferrets (86% nucleotide identity), and another Pneumocystis type in dogs (P. canis Ck2, 81% nucleotide identity) was higher. Golden jackals may be carriers and may play a nonnegligible role in the spread of Pneumocystis spp. Although this finding cannot be directly related to any clinical manifestation or pathologic lesions, a possible role in the exacerbation of different pulmonary disorders should be considered.
Spatial number estimation has a higher linear range than temporal number estimation; differential affordances for subdivision might help to explain why

Estimation of visuospatial number typically has a limited linear range that goes well beyond the subitizing range but typically not beyond 20 items without calibration procedures. Three experiments involving a total of 104 undergraduate students, each tested once, sought to determine if the limit on the linear range represented a capacity limitation of a linear accumulator or might be the result of a strategy based on subdividing spatial displays into potentially subitizable subsets. For visual and auditory temporal numbers for a large range of numbers (2–58; Experiment 1), the (unbiased) linear range was found to be quite restricted (three or four items). Using matched linear spatial number stimuli (Experiment 2), the linear range observed extended to about nine or 10 items. Experiment 3 compared estimates when simultaneous two-dimensional spatial number displays were presented briefly, with estimates for identical displays that accumulated over time. The linear range of estimates for accumulating spatial displays reached only 11 items, whereas that for briefly presented displays extended to about 20 items. These results suggest that the limit on the linear range is not simply a capacity limitation in a linear accumulator. Rather, they support the idea that linear spatial number estimation for the range from five to 20 may be based on subdividing the display into a subitizable number of (potentially) subitizable groups, even if those groups are not outwardly marked.
Elevated ozone decreases the multifunctionality of belowground ecosystems

Elevated tropospheric ozone (O3) affects the allocation of biomass aboveground and belowground and influences terrestrial ecosystem functions. However, how belowground functions respond to elevated O3 concentrations ([O3]) remains unclear at the global scale. Here, we conducted a detailed synthesis of belowground functioning responses to elevated [O3] by performing a meta‐analysis of 2395 paired observations from 222 publications. We found that elevated [O3] significantly reduced the primary productivity of roots by 19.8%, 16.3%, and 26.9% for crops, trees and grasses, respectively. Elevated [O3] strongly decreased the root/shoot ratio by 11.3% for crops and by 4.9% for trees, which indicated that roots were highly sensitive to O3. Elevated [O3] impacted carbon and nitrogen cycling in croplands, as evidenced by decreased dissolved organic carbon, microbial biomass carbon, total soil nitrogen, ammonium nitrogen, microbial biomass nitrogen, and nitrification rates in association with increased nitrate nitrogen and denitrification rates. Elevated [O3] significantly decreased fungal phospholipid fatty acids in croplands, which suggested that O3 altered the microbial community and composition. The responses of belowground functions to elevated [O3] were modified by experimental methods, root environments, and additional global change factors. Therefore, these factors should be considered to avoid the underestimation or overestimation of the impacts of elevated [O3] on belowground functioning. The significant negative relationships between O3‐treated intensity and the multifunctionality index for croplands, forests, and grasslands implied that elevated [O3] decreases belowground ecosystem multifunctionality.
Aortic waveform responses to insulin in late versus early chronotype with metabolic syndrome

Late chronotype (LC) correlates with reduced metabolic insulin sensitivity and cardiovascular disease. It is unclear if insulin action on aortic waveforms and inflammation is altered in LC versus early chronotype (EC). Adults with metabolic syndrome (n = 39, MetS) were classified as either EC (Morning‐Eveningness Questionnaire [MEQ] = 63.5 ± 1.2) or LC (MEQ = 45.5 ± 1.3). A 120 min euglycemic clamp (40 mU/m2/min, 90 mg/dL) with indirect calorimetry was used to determine metabolic insulin sensitivity (glucose infusion rate [GIR]) and nonoxidative glucose disposal (NOGD). Aortic waveforms via applanation tonometry and inflammation by blood biochemistries were assessed at 0 and 120 min of the clamp. LC had higher fat‐free mass and lower VO2max, GIR, and NOGD (between groups, all p ≤ 0.05) than EC. Despite no difference in 0 min waveforms, both groups had insulin‐stimulated elevations in pulse pressure amplification with reduced AIx75 and augmentation pressure (AP; time effect, p ≤ 0.05). However, EC had decreased forward pressure (Pf; interaction effect, p = 0.007) with insulin versus rises in LC. Although LC had higher tumor necrosis factor‐α (TNF‐α; group effect, p ≤ 0.01) than EC, both LC and EC had insulin‐stimulated increases in TNF‐α and decreases in hs‐CRP (time effect, both p ≤ 0.01). Higher MEQ scores related to greater insulin‐stimulated reductions in AP (r = −0.42, p = 0.016) and Pf (r = −0.41, p = 0.02). VO2max correlated with insulin‐mediated reductions in AIx75 (r = −0.56, p < 0.01) and AP (r = −0.49, p < 0.01). NOGD related to decreased AP (r = −0.44, p = 0.03) and Pf (r = −0.43, p = 0.04) during insulin infusion. LC was depicted by blunted forward pressure waveform responses to insulin and higher TNF‐α in MetS. More work is needed to assess endothelial function across chronotypes.
The 4/2 Stochastic Volatility Model

We introduce a new stochastic volatility model that includes, as special instances, the Heston (1993) and the 3/2 model of Heston (1997) and Platen (1997). Our model exhibits important features: first, instantaneous volatility can be uniformly bounded away from zero, and second, our model is mathematically and computationally tractable, thereby enabling an efficient pricing procedure. This called for using the Lie symmetries theory for PDEs; doing so allowed us to extend known results on Bessel processes. Finally, we provide an exact simulation scheme for the model; this is useful in view of the numerical applications.
An Integer Programming Approach to Conversion from Static to Continuous Delivery of Intensity Modulated Radiation Therapy

The aim of this thesis is to generate a starting guess for volumetric modulated arc therapy (VMAT) plan optimization by using data from an intensity modulated radiation therapy (IMRT) plan. We develop a mixed-binary linear programming model, based on choosing segments among a set of predefined segments. The objective is to deliver intensity modulation as similar as possible to the intensity modulation of the IMRT plan. The quality of the solutions is largely dependent on the quality of the predefined segments. However, the model achieves high similarity in intensity modulation when supplied with suitable segments. Unfortunately, high similarity in intensity modulation does not necessarily imply high similarity in dose distribution. In order for the model to generate VMAT plans with acceptable dose distributions the leaf travel between adjacent control points needs to be kept low. The model shows some promising features, but improvements, especially regarding implementation, need to be made in order for the model to be useful.
The effect of phoneme-based auditory training on speech intelligibility in hearing-aid users

Abstract Objective Hearing loss commonly causes difficulties in understanding speech in the presence of background noise. The benefits of hearing-aids in terms of speech intelligibility in challenging listening scenarios remain limited. The present study investigated if phoneme-in-noise discrimination training improves phoneme identification and sentence intelligibility in noise in hearing-aid users. Design Two groups of participants received either a two-week training program or a control intervention. Three phoneme categories were trained: onset consonants (C1), vowels (V) and post-vowel consonants (C2) in C1-V-C2-/i/ logatomes from the Danish nonsense word corpus (DANOK). Phoneme identification test and hearing in noise test (HINT) were administered before and after the respective interventions and, for the training group only, after three months. Study sample Twenty 63-to-79 years old individuals with a mild-to-moderate sensorineural hearing loss and at least one year of experience using hearing-aids. Results The training provided an improvement in phoneme identification scores for vowels and post-vowel consonants, which was retained over three months. No significant performance improvement in HINT was found. Conclusion The study demonstrates that the training induced a robust refinement of auditory perception at a phoneme level but provides no evidence for the generalisation to an untrained sentence intelligibility task.
PRKCE non-coding variants influence on transcription as well as translation of its gene

ABSTRACT Untranslated regions of the gene play a crucial role in gene expression regulation at mRNA and protein levels. Mutations at UTRs impact expression by altering transcription factor binding, transcriptional/translational efficacy, miRNA-mediated gene regulation, mRNA secondary structure, ribosomal translocation, and stability. PKCε, a serine/threonine kinase, is aberrantly expressed in numerous diseases such as cardiovascular disorders, neurological disorders, and cancers; its probable cause is unknown. Therefore, in the current study, the influence of PRKCE 5’-and 3'UTR variants was explored for their potential impact on its transcription and translation through several bioinformatics approaches. UTR variants data was obtained through different databases and initially evaluated for their regulatory function. Variants with regulatory function were then studied for their effect on PRKCE binding with transcription factors (TF) and miRNAs, as well as their impact on mRNA secondary structure. Study outcomes indicated the regulatory function of 73 5'UTR and 17 3'UTR variants out of 376. 5'UTR variants introduced AP1 binding sites and promoted the PRKCE transcription. Four 3'UTR variants introduced a circular secondary structure, increasing PRKCE translational efficacy. A region in 5'UTR position 45,651,564 to 45,651,644 was found where variants readily influenced the miRNA-PRKCE mRNA binding. The study further highlighted a PKCε-regulated feedback loop mechanism that induces the activity of TFs, promoting its gene transcription. The study provides foundations for experimentation to understand these variants’ role in diseases. These variants can also serve as the genetic markers for different diseases’ diagnoses after validation at the cell and population levels.
On moments of Cantor and related distributions

We provide several simple recursive formulae for the moment sequence of infinite Bernoulli convolution. We relate moments of one infinite Bernoulli convolution with others having different but related parameters. We give examples relating Euler numbers to the moments of infinite Bernoulli convolutions. One of the examples provides moment interpretation of Pell numbers as well as new identities satisfied by Pell and Lucas numbers.
Performance analysis of digital silicon photomultipliers for PET

A silicon photomultiplier (SiPM) with electronics integrated on cell level has been developed by Philips Digital Photon Counting. The device delivers a digital signal of the detected photon counts and their time stamp, making it a potential candidate for positron emission tomography (PET) applications. Several operational parameters of the specifically developed acquisition protocol can be adjusted to optimize the photon detection. In this work, the combination of five different parameters (trigger scheme, validation scheme, cell inhibition, temperature and excess bias voltage) is analyzed. Their impact on both the intrinsic as well as the PET-oriented sensor's performance is studied when coupled to two different PET candidate scintillators, GAGG and LYSO (2 × 2 × 6 mm3). The results show that SiPM intrinsic properties such as breakdown voltage temperature coefficient (20 mV/K) and optical crosstalk (20%) are similar to state-of-the-art analog devices. The main differences are induced by the logic of the acquisition sequence and its parameters. The sensor's dark-count-rate (DCR) is 770 kHz/mm2 at 24°C and 100% active cells. It can be reduced through cell inhibition and lower temperatures (ca. 2 orders of magnitude at 0°C and 20% cell inhibition). DCR reduction is necessary to avoid acquiring dark-count-triggered and validated events, causing loss of detection sensitivity. The typical time fraction spent with these events is 42.5% (GAGG) and 35.5% (LYSO). Increasing percentages of cell inhibition affect the photodetection efficiency and with it the energy resolution and the coincidence time resolution (CTR). At 5.6 °C and 10% cell inhibition, the measured energy resolution is 11.9% and 13.5% (FWHM, saturation corrected) and a FWHM CTR of 458 ps and 177 ps is achieved, for GAGG and LYSO respectively. With the implemented setup, the optimum configuration for PET, in terms of sensitivity, energy resolution and CTR, is trigger scheme 1, validation scheme 8, 10% cell inhibition and 3.0 V excess bias. Cooling the sensor to 0°C considerably improves the device's performance.