Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in Soil Fertility Parameters in Response to Irrigation of Forage Crops with Secondary Treated Wastewater

Field experiments were conducted to evaluate the effect of irrigation with treated wastewater on soil fertility and chemical characteristics. Three field experiments were conducted at a farmer's field near Ramtha Wastewater Treatment Plant. Corn (Zea mays) was planted for two seasons as a summer crop while vetch (Vicia sativa) for one season as a winter crop. Plots were irrigated with either potable water (PW) or wastewater (WW) in amount according to the following treatments: i) potable water equivalent to 100% class A pan reading (PW); ii) wastewater equivalent to 100% class A pan reading (WW1); iii) PW with application fertilizer equivalent to N and P content of WW (PWF) and iv) wastewater equivalent to 125% class A pan reading (WW2). Treatments were replicated 4 times in a randomized complete block design. Soil samples were taken before and at the end of the growing season and were analyzed for soil parameters. WW samples were taken and analyzed periodically for major characteristics. WW analysis indicates inefficient treatment and high values of Biological Oxygen Demand, salt content and reduced form of nitrogen. The results of the field experiments indicate that WW irrigation decreased soil pH and increased soil salinity, soil phosphorus (P), potassium (K), iron (Fe), and manganese (Mn) levels. Soil organic matter increased only in the topsoil and by the highest rate of WW irrigation. This effect could be attributed either directly through the addition of the nutrients and organic compounds to the soil or indirectly through enhancing solubility of soil nutrients. Soil zinc (Zn) and copper (Cu) were not significantly affected by WW irrigation. It can be concluded that secondary treated WW can improve soil fertility parameters, however, more efficient treatment is recommended to reduce salt content. In addition, proper irrigation management and periodic monitoring of soil quality parameters are required to minimize adverse effect on the soil.
Protein secondary structure from FT-IR spectroscopy : correlation with dihedral angles from three-dimensional Ramachandran plots

The frequency of the so-called "amide I" band (amide C=O stretching vibration, vC=O) of proteins is discussed in terms of the dihedral angles of the various secondary structures present within proteins. We propose that in the case of intra- or intermolecular hydrogen-bonded amide carbonyl groups the frequency of this absorption can be directly related to the , ψ angles of the amide moieties for the major secondary structures. Amide I bands at frequencies above those found for non-hydrogen bonded amide carbonyl groups are rationalized in terms of a change in the third dihedral angle, ω. Rotation around the amide C—N bond in sterically demanding structures, such as turns where ω deviates from 180°, is expected to cause an increase in the electron density of the amide carbonyl groups and so increase vC=O to frequencies greater than that seen for unperturbed carbonyl groups. Key words: FT-IR spectroscopy, proteins, structure, dihedral angles.
UV- or Visible-Light-Induced Degradation of X3B on TiO2 Nanoparticles: The Influence of Adsorption

Photodegradation of a textile dye X3B using either UV (λ ≥ 320 nm) or visible light (λ ≥ 450 nm) over three catalysts of highly adsorptive TiO2 nanoparticles in water has been examined. All the adsorption isotherms demonstrated the Langmuir type behavior. The common observation was confirmed that for all the reactions induced by UV or visible light, the apparent initial rate of X3B loss in the aqueous phase increased with the initial equilibrated concentration of X3B. However, this correlation was changed when the rate was determined by the decreased concentration both in the aqueous phase and on the catalyst surface. This increase of real initial rate with the initial equilibrated concentration was observed only in the visible-light-induced reaction over TiO2 of Degussa P25. For all the other reactions, especially under UV irradiation, the real initial rate was found to increase only initially and then decrease with the initial equilibrated concentration. The result suggests that there is a screening eff.
Phenotypic features of cancer cachexia‐related loss of skeletal muscle mass and function: lessons from human and animal studies

Cancer cachexia is a complex multi‐organ catabolic syndrome that reduces mobility, increases fatigue, decreases the efficiency of therapeutic strategies, diminishes the quality of life, and increases the mortality of cancer patients. This review provides an exhaustive and comprehensive analysis of cancer cachexia‐related phenotypic changes in skeletal muscle at both the cellular and subcellular levels in human cancer patients, as well as in animal models of cancer cachexia. Cancer cachexia is characterized by a major decrease in skeletal muscle mass in human and animals that depends on the severity of the disease/model and the localization of the tumour. It affects both type 1 and type 2 muscle fibres, even if some animal studies suggest that type 2 muscle fibres would be more prone to atrophy. Animal studies indicate an impairment in mitochondrial oxidative metabolism resulting from a decrease in mitochondrial content, an alteration in mitochondria morphology, and a reduction in mitochondrial metabolic fluxes. Immuno‐histological analyses in human and animal models also suggest that a faulty mechanism of skeletal muscle repair would contribute to muscle mass loss. An increase in collagen deposit, an accumulation of fat depot outside and inside the muscle fibre, and a disrupted contractile machinery structure are also phenotypic features that have been consistently reported in cachectic skeletal muscle. Muscle function is also profoundly altered during cancer cachexia with a strong reduction in skeletal muscle force. Even though the loss of skeletal muscle mass largely contributes to the loss of muscle function, other factors such as muscle–nerve interaction and calcium handling are probably involved in the decrease in muscle force. Longitudinal analyses of skeletal muscle mass by imaging technics and skeletal muscle force in cancer patients, but also in animal models of cancer cachexia, are necessary to determine the respective kinetics and functional involvements of these factors. Our analysis also emphasizes that measuring skeletal muscle force through standardized tests could provide a simple and robust mean to early diagnose cachexia in cancer patients. That would be of great benefit to cancer patient's quality of life and health care systems.
Production of probiotic ice cream

Probiotic ice cream was manufactured by mixing fortified milk fermented with probiotic strains with an ice cream mix, followed by freezing. The probiotic ice cream was evaluated for chemical properties, cultures survival and sensory characteristics during 12 week of frozen storage at -26°C. Analysis of ice cream mixes showed higher acidity and viscosity in the case of mixes containing probiotic bacteria. There was no effect on specific gravity as well as weight per gallon of bio-ice cream mixes. Freezing point of mixes decreased in all bio-ice cream compared to control. Ice cream analysis showed an increase in both values of specific gravity and weight per gallon with adding the probiotic cultures. Overrun percent has affected with the addition of probiotic cultures. All treatments showed slightly faster melting than control. Initial freezing of ice cream mix followed by hardening caused a reduction of less than one log cycle in viable counts of probiotics. The viable counts decreased by 2.23, 1.68, 1.54, 1.23 and 1.77 log cfu/g for Lactobacillus acidophilus, Bifidobacterium bifidum, Lactobacillus reuteri, Lactobacillus gasseri and Lactobacillus rhamnosus, respectively, during 12 weeks of frozen storage. Although there was a decrease in the number of viable cells, the ice cream may be considered as a probiotic food during 12 weeks of storage, since the remained was above the recommended minimum limit of 10 6 cfu/g. All the ice cream samples received a high score in the organoleptic evaluation. Lactobacillus reuteri containing ice cream was judged to be more sour and attained a higher score for probiotic flavour.
Intrauterine Zika virus infection: review of the current findings with emphasis in the prenatal and postnatal brain imaging diagnostic methods

Abstract Zika virus (ZIKV) is a widespread flavivirus transmitted to humans through the bite of Aedes mosquitoes. The number of ZIKV cases increased significantly between 2015 and 2016, and Brazil was the first to report autochthonous transmission of infection. The main neurological disorder related to ZIKV infection is microcephaly. Fetal magnetic resonance imaging (MRI) is the gold standard examination for the analysis of fetal brain infection, followed by obstetric ultrasonography. Cerebral atrophy, intracranial calcifications, ventriculomegaly, cerebellar, and brain gyrus abnormalities are some of the most common findings. Postnatal MRI shows high sensitivity and specificity. Corpus callosum abnormalities, cerebellar hypoplasia, and choroid plexus dilation can be also observed. We present a review of congenital ZIKV infection with emphasis on pre and postnatal brain findings using ultrasonography, MRI, computed tomography, and three-dimensional reconstruction models.
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification

High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in these large datasets, in particular the identification of therapeutic antibodies (Abs) or those associated with disease exposure and protection. Here, we describe our efforts to use artificial intelligence (AI)-based image-analyses for prospective classification of Abs based solely on sequence information. We hypothesized that Abs recognizing the same part of an antigen share a limited set of features at the binding interface, and that the binding site regions of these Abs share share common structure and physicochemical property patterns that can serve as a “fingerprint” to recognize uncharacterized Abs. We combined large-scale sequence-based protein-structure predictions to generate ensembles of 3-D Ab models, reduced the Ab binding interface to a 2-D image (fingerprint), used pre-trained convolutional neural networks to extract features, and trained deep neural networks (DNNs) to classify Abs. We evaluated this approach using Ab sequences derived from human HIV and Ebola viral infections to differentiate between two Abs, Abs belonging to specific B-cell family lineages, and Abs with different epitope preferences. In addition, we explored a different type of DNN method to detect one class of Abs from a larger pool of Abs. Testing on Ab sets that had been kept aside during model training, we achieved average prediction accuracies ranging from 71–96% depending on the complexity of the classification task. The high level of accuracies reached during these classification tests suggests that the DNN models were able to learn a series of structural patterns shared by Abs belonging to the same class. The developed methodology provides a means to apply AI-based image recognition techniques to analyze high-throughput B-cell sequencing datasets (repertoires) for Ab classification.
De Novo Malignancies after Kidney Transplantation

Cancer is an important outcome after kidney transplantation because it is the second leading cause of death in most Western countries. The excess risk of cancer after transplantation is approximately two to three times higher than the age- and sex-matched general population, driven largely by viral- and immune-related cancers. Once cancer develops, outcomes are generally poor, particularly for those with melanoma, renal cell carcinoma, and post-transplant lymphoproliferative disease. More importantly, effective screening and treatment strategies are limited in this high-risk population. In this review, we begin with a patient’s journey that maps the experience of living with a kidney transplant and understand the patient’s knowledge, education, and experience of cancer in the context of transplantation. The epidemiology and burden of cancer in recipients of kidney transplants, along with the up-to-date screening and treatment strategies, are discussed. We also focus on the current understanding of optimal care for recipients of kidney transplants who are living with cancer from the patients’ perspectives.
Effects of a reduced-sodium added-potassium salt substitute on blood pressure in rural Indian hypertensive patients: a randomized, double-blind, controlled trial.

BACKGROUND High salt intake is a major modifiable risk factor of hypertension which is prevalent in India. It is not yet clear if salt substitutes reduce blood pressure (BP) among Indian hypertensive patients. OBJECTIVES Examine the acceptability, usage, and BP effects of a reduced-sodium and added-potassium salt substitute among hypertensive patients. METHODS We enrolled 502 participants with hypertension (aged 61.6 ± 12.0 y, 58.8% women) from 7 villages in rural India. Participants were randomly assigned to receive either regular salt (100% sodium chloride) or the salt substitute (70% sodium chloride/30% potassium chloride blend), and advised to replace all home salt use. The primary outcome was the change in systolic BP (SBP) from baseline to 3 mo comparing the salt substitute and regular salt groups. Secondary outcomes included the change in diastolic BP (DBP), 24-h urinary biomarkers, and self-reported use and satisfaction with the study salt provided. RESULTS A total of 494 (98%) participants completed 1 mo and 476 (95%) participants completed the 3-mo follow-up. At 3 mo, the salt substitute intervention significantly decreased the average SBP by 4.6 mmHg (95% CI: 3.0, 6.2, P < 0.001) and DBP by 1.1 mmHg (95% CI: 0.2, 2.1 mmHg, P = 0.02). There was a significant increase in 24-h urinary potassium excretion in the salt substitute group by 0.24 g/d (95% CI: 0.12, 0.35 g/d, P < 0.001) and a decrease in the urinary sodium to potassium ratio by 0.71 (95% CI: 0.55, 0.87, P < 0.0001) compared with the control group. Participants reported that they used the study salt nearly every day of the week (mean ± SD, 6.3 ± 1.8 d) and rated the taste of the study salts similarly. CONCLUSION The reduced-sodium added-potassium salt led to a substantial reduction in SBP in hypertensive patients, supporting salt substitution as an effective, low-cost intervention for BP lowering in rural India. This trial was registered at clinicaltrials.gov as NCT03909659.
Influence of Allyl Isothiocyanate on the Soil Microbial Community Structure and Composition during Pepper Cultivation

Allyl isothiocyanate (AITC), as a fumigant, plays an important role in soil control of nematodes, soilborne pathogens, and weeds, but its effects on soil microorganisms are unclear. In this study, the effects of AITC on microbial diversity and community composition of Capsicum annuum L. soil were investigated through Illumina high-throughput sequencing. The results showed that microbial diversity and community structure were significantly influenced by AITC. AITC reduced the diversity of soil bacteria, stimulated the diversity of the soil fungal community, and significantly changed the structure of fungal community. AITC decreased the relative abundance of dominant bacteria Planctomycetes, Acinetobacter, Pseudodeganella, and RB41, but increased that of Lysobacter, Sphingomonas, Pseudomonas, Luteimonas, Pseudoxanthomonas, and Bacillus at the genera level, while for fungi, Trichoderma, Neurospora, and Lasiodiplodia decreased significantly and Aspergillus, Cladosporium, Fusarium, Penicillium, and Saccharomyces were higher than the control. The correlation analysis suggested cellulase had a significant correlation with fungal operational taxonomic units and there was a significant correlation between cellulase and fungal diversity, while catalase, cellulose, sucrase, and urease were the major contributors in the shift of the community structure. Our results will provide useful information for the use of AITC in the assessment of environmental and ecological security.
Impact of diverse aortic pathologies on outcomes after transapical transcatheter aortic valve replacement

Some patients who undergo transcatheter aortic valve replacement (TAVR) have a concomitant diverse aortic pathologies (AP). They are usually considered high‐risk candidates for the procedure and require further assessment to determine the best vascular approach. The impact of these AP on TAVR is not well known as the information is scarce. We aimed to evaluate midterm clinical impact of different AP after transapical (TA)‐TAVR.
Cognitive training interventions for dementia and mild cognitive impairment in Parkinson's disease - A cochrane review summary with commentary.

BACKGROUND The majority of people living with Parkinson's disease will develop impairments in cognition. These impairments are associated with a reduced quality of life. OBJECTIVE The Cochrane Review aimed to investigate whether cognitive training improves cognition in people with Parkinson's disease and mild cognitive impairments or dementia. METHODS A Cochrane Review by Orgeta et al. was summarized with comments. RESULTS The review included seven studies with a total of 225 participants. There was no evidence for improvements in global cognition when cognitive training was compared to control conditions. Observed improvements in attention and verbal memory measures after cognitive training could not be confirmed in a subsequent sensitivity analysis. There was no evidence for benefits in other cognitive domains or quality of life measures. The certainty of the evidence was low for all comparisons. CONCLUSIONS The effectiveness of cognitive training for people with Parkinson's disease and cognitive impairments remains inconclusive. There is a pressing need for adequately powered trials with higher methodological quality.
Superhydrophobic surfaces: from structural control to functional application

A superhydrophobic surface is a surface with a water contact angle close to or higher than 150°. In this feature article, we review the historical and present research on superhydrophobic surfaces, including the characterization of superhydrophobicity, different ways to fabricate rough surfaces, and low-surface-energy modifications on inorganic and organic rough surfaces. It is the combination of surface roughness and low-surface-energy modification that leads to superhydrophobicity. Notably, research on superhydrophobic surfaces has not only fundamental interest but various possible functional applications in micro- and nano-materials and devices.
The impact of micronutrient deficiency on pregnancy complications and development origin of health and disease

Due to the spread of the western style diet, which is characterized by high intake of processed food, micronutrients (vitamins and minerals) deficiency is increasing in the Japanese population of all ages and genders. During pregnancy, the elevated demand for micronutrients put pregnant women at even higher risk of micronutrients deficiency. Some micronutrients are relatively famous such that women with reproductive age are recommended to take folic acid supplementation for the prevention of neural tube defect. However, it is not generally known that folate is also important for fetal growth throughout the pregnancy course and for prevention of pregnancy complications, and that pregnant women should continue to take supplementation during pregnancy and lactation. The types of micronutrients and the duration of supplementation are both important factors to maintain normal pregnancies. This review focused on four micronutrients that are commonly deficient in Japanese pregnant women, folate, vitamin B12, vitamin D, calcium, and magnesium. The detrimental effects of homocysteine accumulation associated with the above micronutrient defects and its link to catechol‐o‐methyltransferase insufficiency are described. We also discussed possible molecular mechanisms of pregnancy complications and the development origin of health and disease (DOHaD) regarding micronutrient deficiencies from the point of view of one carbon metabolism.
Attempt to approach the role of phenolic phenylpropenol structures in the photoyellowing of softwood mechanical pulps

Three biphenyl (I, II, III) compounds and a benzylarylether (IV) compound were synthesized to detect and quantify the presence of phenolic phenylpropenols in unbleached, peroxide-bleached, or sodium borohydride-reduced mechanical softwood pulps. The methodology used is based on a gas chromatography  mass spectrometry search of the prepared compounds in the residue obtained after ethylation, thioacidolysis, and desulfurization of the pulps. Detection of biphenyl I (4 × 106 mol g1) in unbleached and NaBH4-reduced pulps is indicative of the presence of phenolic coniferaldehyde units in these pulps. Traces of biphenyl II, found in the peroxide-bleached pulp, probably came from ferulic acid units formed by oxidation of coniferaldehyde by H2O2. No biphenyl ether III or benzylaryl ether IV were detected in the three pulps. This result indicates that phenolic phenylpropenol units are not present in softwood mechanical pulps and do not contribute to the fast part of their photoyellowing.Key words: mechanical pu.
Use of NAD tagSeq II to identify growth phase-dependent alterations in E. coli RNA NAD+ capping

Significance Some RNAs in both prokaryotes and eukaryotes were recently found to contain the NAD+ cap, indicating a novel mechanism in gene regulation through noncanonical RNA capping. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry has been used to label NAD+-capped RNAs (NAD-RNAs) for their identification. However, copper-caused RNA fragmentation/degradation interferes with the analysis. We developed the NAD tagSeq II method for transcriptome-wide NAD-RNA analysis based on copper-free, strain-promoted azide-alkyne cycloaddition (SPAAC) click chemistry. This method was used to compare NAD-RNA and total transcriptome profiles in Escherichia coli. Our study reveals genome-wide alterations in E. coli RNA NAD+ capping in different growth phases and indicates that NAD-RNAs could be the primary form of transcripts from some genes under certain environments. Recent findings regarding nicotinamide adenine dinucleotide (NAD+)-capped RNAs (NAD-RNAs) indicate that prokaryotes and eukaryotes employ noncanonical RNA capping to regulate gene expression. Two methods for transcriptome-wide analysis of NAD-RNAs, NAD captureSeq and NAD tagSeq, are based on copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry to label NAD-RNAs. However, copper ions can fragment/degrade RNA, interfering with the analyses. Here we report development of NAD tagSeq II, which uses copper-free, strain-promoted azide-alkyne cycloaddition (SPAAC) for labeling NAD-RNAs, followed by identification of tagged RNA by single-molecule direct RNA sequencing. We used this method to compare NAD-RNA and total transcript profiles of Escherichia coli cells in the exponential and stationary phases. We identified hundreds of NAD-RNA species in E. coli and revealed genome-wide alterations of NAD-RNA profiles in the different growth phases. Although no or few NAD-RNAs were detected from some of the most highly expressed genes, the transcripts of some genes were found to be primarily NAD-RNAs. Our study suggests that NAD-RNAs play roles in linking nutrient cues with gene regulation in E. coli.