Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of the amounts of phosphate fertilizer, and of the proportions of water-soluble phosphate in the fertilizers tested on the phosphorus nutrition of sorghum

SUMMARY A field experiment was made with sorghum hybrid CSH-1 during the rainy seasons of 1968 and 1969 on a sandy loam soil to study the influence of amounts and sources of phosphate fertilizer on phosphorus nutrition. Concentration of P in the crop and uptake increased with increasing amounts of phosphate and with increasing proportions of water-soluble P in triple superphosphate-dicalcium phosphate and triple superphosphate-rock phosphate mixtures. Relative effectiveness values were calculated from P uptake at harvest by a multiple regression method. For triple superphosphate, nitrophosphate (30% water soluble P), dicalcium phosphate and rock phosphate (from Jordan) the values were respectively, 100, 74, 61 and 22.
From Library Screening to Microarray Technology: Strategies to Determine Gene Expression Profiles and to Identify Differentially Regulated Genes in Plants.

Hybridization to DNA microarrays and high density membrane filters, serial analysis of gene expression (SAGE), the cDNA-AFLP technique, restriction fragment-coupled differential display (RC4D), differential display reverse transcription PCR (DDRT-PCR) and also the differential screening of standard and subtracted cDNA libraries are techniques being used extensively to determine transcription patterns or to identify differentially regulated genes in plants and other organisms. In this review, commonly used display systems are evaluated and compared. The general principles on which the different techniques are based and which determine their potential and their limitations are described. Performance aspects of each method are discussed, and existing applications of each method are briefly surveyed. Some typical examples are considered to illustrate how differential display systems have been applied to plants and to what extent these techniques have contributed to our understanding of plant gene expression.
Mitochondrial DNA Variation and Systematics of the Guanaco (Lama guanicoe, Artiodactyla: Camelidae)

Abstract Guanacos (Lama guanicoe) are the most important native herbivorous species in the South American steppes and the dominant ungulate in a fauna rich in rodents but poor in large mammal species. Between 2 and 4 subspecies are usually recognized within Lama guanicoe, based on subtle morphological differences and geographic distribution. To evaluate whether molecular variation is consistent with the latter hypotheses, we analyzed the complete cytochrome-b and partial control region mitochondrial DNA sequences of L. guanicoe from 22 localities in Peru, Bolivia, Argentina, and Chile. Sequence analyses of both genes support the monophyly of the species but failed to distinguish the occurrence of subspecies along the geographic range. Despite that, the northernmost populations (Peru and northern Chile) showed some degree of genetic differentiation with respect to southern representatives from Argentina, Bolivia, and rest of Chile. Analysis of genetic diversity also showed a strong signal of past low population size and a recent population expansion.
SPAWNING SOUNDS IN WHITEMOUTH CROAKER (SCIAENIDAE): SEASONAL AND DAILY CYCLES

ABSTRACT Recordings with a hydrophone deployed from a boat and the shore revealed that the sciaenid Whitemouth Croaker Micropogonias furnieri produces a seasonal and daily characteristic courtship/spawning sound in the Pando stream mouth on the Rio de la Plata estuary during the spawning season from November to March. Recordings were made at five stations. The drumming sound was qualitatively rated on scale of 0–4, according to criteria proposed by Connaughton & Taylor (1995). Recordings of 5 marked individuals were made in a 3000-1 canvas tank in the laboratory for three months (December 2006–March 2007). The drumming or advertisement call of Whitemouth Croaker was strongly seasonal, appearing in October, increasing to a peak in January—March, and then disappearing abruptly in April, in coincidence with the spawning season and with gonadosomatic index (GSI). Daily drumming activity showed two peaks through the day, increasing in the early morning between 07:00 to 10:00 h and in the evening between 17:00 to 23:00 h.
Response of Seed Germination and Seedling Growth to Sand Burial of Two Dominant Perennial Grasses in Mu-Us Sandy Grassland, Semiarid China

Abstract Sand burial is an important selective pressure for growth, survival, and distribution of sand dune plants. Its effects on seed germination and seedling establishment, however, for different species are quite different. Experiments were conducted in the Mu-Us Sandy Grassland of North China to determine the effects of sand burial on seed germination and seedling growth of dominant perennial grasses Psammochloa villosa (Trin.) Bor and Leymus secalinus (Georgi) Tzvel. Small, medium, and large seeds of P. villosa and small and large seeds of L. secalinus were buried at 0-, 1-, 2-, 4-, 6-, and 8-cm depths in sand. P. villosa seed germination and seed dormancy in sand were significantly influenced by sand burial depth but not by seed size, whereas seed germination and seed dormancy of L. secalinus were significantly influenced by both sand burial depth and seed size. Emergence percentages for large seeds were higher than those for smaller seeds, suggesting that larger seeds are ecologically better adapted to dune habitats. Seeds that did not germinate in sand were in enforced dormancy and formed a soil seedbank, which can enhance plant survival on sand dunes. One-week-old and 2-wk-old P. villosa seedlings could tolerate 75% and 100% of their shoot height of sand burial, respectively, and the shoot elongation growth was enhanced by the burial stress. Both 1-wk-old and 2-wk-old seedlings of L. secalinus only tolerated up to 75% sand burial. The growth of L. secalinus seedling was inhibited by sand burial due to the decreased biomass and slow shoot elongation. The lack of tolerance of seedlings of this species to total sand burial might restrict its distribution on sand dunes.
Antioxidant Activities of Aqueous Extract from Cultivated Fruit-bodies of Cordyceps militaris (L.) Link In Vitro

Biological antioxidants extracted from plants and fungi have potential abilities to scavenge free radicals and inhibit lipid peroxidation, playing important roles in preventing diseases, for example, cancer, and aging induced by reactive oxygen species, which may cause oxidative damage to DNA, proteins and other macromolecules. The antioxidant potency of cultivated fruit-bodies of Cordyceps militaris (L.) Link was investigated in this study. Five established in vitro systems were employed, including the 1,1-diphenyl-2-picryldrazyl (DPPH) free radical scavenging, hydroxyl radical eliminating, iron chelating, inhibition of linoleic acid lipid peroxidation and reducing power. The aqueous extract from cultivated fruit-bodies was subjected to the test of amino acid, polysaccharide and mannitol. Ascorbic acid (Vc), butylated hydroxytoluene (BHT) and ethylenediaminetetraacetic acid (EDTA) were used as positive controls for comparisons. Among the assays, the aqueous extract of C. militaris fruit-bodies shows a significant scavenging effect on DPPH, eliminating the capability on hydroxyl radicals and the chelating effect on ferrous iron. The extract also shows positive results of inhibiting linoleic acid lipid peroxidation and reducing power. (Managing editor: Wei Wang)
Epitope based peptide vaccine against SARS-COV2: an immune-informatics approach

Abstract World is witnessing exponential growth of SARS-CoV2 and fatal outcomes of COVID 19 has proved its pandemic potential already by claiming more than 3 lakhs deaths globally. If not controlled, this ongoing pandemic can cause irreparable socio-economic and psychological impact worldwide. Therefore a safe and effective vaccine against COVID 19 is exigent. Recent advances in immunoinformatics approaches could potentially decline the attrition rate and accelerate the process of vaccine development in these unprecedented times. In the present study, a multivalent subunit vaccine targeting S2 subunit of the SARS-CoV2 S glycoprotein has been designed using open source, immunoinformatics tools. Designed construct comprises of epitopes capable of inducing T cell, B cell (Linear and discontinuous) and Interferon γ. physiologically, vaccine construct is predicted to be thermostable, antigenic, immunogenic, non allergen and non toxic in nature. According to population coverage analysis, designed multiepitope vaccine covers 99.26% population globally. 3D structure of vaccine construct was designed, validated and refined to obtain high quality structure. Refined structure was docked against Toll like receptors to confirm the interactions between them. Vaccine peptide sequence was reverse transcribed, codon optimized and cloned in pET vector. Our in-silico study suggests that proposed vaccine against fusion domain of virus has the potential to elicit an innate as well as humoral immune response in human and restrict the entry of virus inside the cell. Results of the study offer a framework for in-vivo analysis that may hasten the process of development of therapeutic tools against COVID 19. Communicated by Ramaswamy H. Sarma
Exchange of Clinical and Omics Data According to FAIR Principles: A Review of Open Source Solutions

Abstract Background Due to the ongoing increase and importance of the sustainable reusability of data, the findable, accessible, interoperable, reusable or FAIR principles were developed which are also relevant in translational research. Objectives The study aims at identification of platforms by literature search that are suitable for implementation in translational research, in particular with regard to their FAIRness. Methods The collected information is summarized and compared. Results Platforms have been identified which are suitable for linking with other translational platforms with regard to documentation, long-term archiving, and processing as well as for FAIR handling of bioinformatic data. Conclusion There are already platforms in the translational environment that take FAIR principles into account and thus improve translational research. Due to the specialization of the research platforms and the fact that FAIR are only principles and not standards, the platforms have to be examined in individual cases to see whether and how they can be integrated with other platforms.
The development of a speech sound screening test for European French-speaking monolingual and bilingual children

Abstract Purpose This study presents normative data on a screening test, referred to as the Dépistage Rapide Articulation et Phonologie (DRAP), designed to detect European French-speaking children who are at risk for having speech sound disorders. Method The test consists of 20 words which contain late-acquired phonological features such as medial and final /r/, consonant clusters, /s/C sequences, and alveolar and post-alveolar fricatives. The test was given to 196 children, monolingual and bilingual, living in Geneva and San Francisco, and ranging in age from 2.11 through to 6.11. Our analyses examined the influence of bilingualism, context (Geneva or San Francisco), gender and age on the test scores and also looked at the influence of these factors on phonological features in the test. Result There were no strong effects of bilingualism, context, and gender on the test results but strong effects of age. Validity and internal consistency of the test were in the acceptable range. A focus on phonological features indicated that children had difficulty with final clusters and post-alveolar fricatives. Conclusion The study provides encouraging results for the use of this test as a screening measure with French-speaking children.
Cognition, function and awareness of disease impact in early Parkinson’s and Huntington’s disease

Abstract Purpose Patients with Parkinson’s and Huntington’s Disease (PD and HD) present impairments in cognitively challenging everyday activities. This study contrasts these two basal ganglia disorders on the ability to perform daily life- like tasks and their level of awareness regarding the disease impact on function. Methods 19 controls, 10 early-onset PD, 20 early stage PD, and 15 early manifest HD patients were compared in the “EcoKitchen,” a virtual reality task with increasing executive load, the “Behavioural Assessment of Dysexecutive Syndrome battery – BADS,” and “The Adults and Older Adults Functional Assessment Inventory – IAFAI,” a self-report functional questionnaire. The EcoKitchen clinical correlates were investigated. Results All clinical groups presented slower EcoKitchen performance than controls, however, only HD patients showed decreased accuracy. HD and PD patients exhibited reduced BADS scores compared to the other study participants. Importantly, on the IAFAI, PD patients signalled more physically related incapacities and HD patients indicated more cognitively related incapacities. Accordingly, the EcoKitchen performance was significantly associated with PD motor symptom severity. Conclusions Our findings suggest differential disease impact on cognition and function across PD and HD patients, with preserved awareness regarding disease- related functional sequelae. These observations have important implications for clinical management, research and rehabilitation. Implications for rehabilitation Patients with early stage Parkinson’s and Huntington’s disease have diagnosis-specific impairments in the performance of executively demanding everyday activities and, yet, show preserved awareness about the disease impact on their daily life. An active involvement of patients in the rehabilitation process should be encouraged, as their appraisal of the disease effects can help on practical decisions about meaningful targets for intervention, vocational choices, quality-of-life issues and/or specific everyday skills to boost. The EcoKitchen, a non-immersive virtual reality task, can detect and quantify early deficits in everyday-like tasks and is therefore a valuable tool for assessing the effects of rehabilitation strategies on the functional cognition of these patients. Rehabilitation efforts in the mild stages of Parkinson’s and Huntington’s disease should be aware of greater time needs from the patients in the performance of daily life tasks, target executive skills, and give a more prominent role to patients in symptoms report and management.
Mobile phone use pattern and addiction in relation to depression and anxiety.

Background University students with heavy smartphone use are vulnerable to smartphone addiction that could be related to depression and trait anxiety. Aims To assess gender differences in patterns of smartphone use and addiction in relation to depression and trait anxiety among Saudi university students. Methods This was a cross-sectional study of 1513 students of Taif University, Saudi Arabia. A self-reported questionnaire was used to collect demographic data and data on pattern of smartphone use. The Problematic Use of Mobile Phones (PUMP) scale was used to determine smartphone addiction. The Arabic validated version of the Taylor Manifest Anxiety Scale and Beck Depression Inventory were used to assess trait anxiety and depression, respectively. Results A female predominance was found for: prevalence of depression and trait anxiety, PUMP scores, duration of daily mobile use and number of daily calls. A significant positive correlation was found between PUMP score and depression and trait anxiety scores, duration of owning a smartphone, and average duration of each daily call. The PUMP scores were significantly higher in 6th year students, those from the theoretical college, single students, and students who used a smartphone for > 4 hours/day. Conclusions Smartphone addiction is a major problem among Saudi university students, and it is associated with depression and trait anxiety. Future studies should aim to establish the best interventions to protect university students from the negative effects of smartphones.
Molecular Docking Explains Atomic Interaction between Plant-originated Ligands and Oncogenic E7 Protein of High Risk Human Papillomavirus Type 16

Cervical cancer caused by Human papillomavirus (HPV) is one of the leading causes of cancer mortality in women worldwide, particularly in the developing countries. In the last few decades, various compounds from plant origin such as Curcumin, Epigallocatechin gallate (EGCG), Jaceosidin, Resveratrol etc. have been used as anti cancer therapeutic agents. Different studies have shown these plant-originated compounds are able to suppress HPV infection. The E6 and E7 oncoproteins of high-risk HPV play a key role in HPV related cancers. In this study, we explored these ligands from plants origin against E7 oncoprotein of high risk HPV 16, which is known to inactivate tumor suppressor pRb protein. A robust homology model of HPV 16 E7 was built to foresee the interaction mechanism of E7 oncoprotein with these ligands using structure-based drug designing approach. Docking studies demonstrate the interaction of these ligands with pRb binding site of E7 protein by residues Tyr52, Asn53, Val55, Phe57, Cys59, Ser63, Thr64, Thr72, Arg77, Glu80 and Asp81 and help restoration of pRb functioning. This in silico based atomic interaction between these ligands and E7 protein may assist in validating the plant- originated ligands as effective drugs against HPV.
Skin colour and vitamin D: An update

Homo sapiens evolved in East Africa and had dark skin, hair, and eyes, in order to protect against deleterious consequences of intensive UV radiation at equatorial latitudes. Intensive skin pigmentation was thought to bear the risk of inefficient vitamin D3 synthesis in the skin. This initiated the hypothesis that within the past 75 000 years, in which humans migrated to higher latitudes in Asia and Europe, the need for vitamin D3 synthesis served as an evolutionary driver for skin lightening. In this review, we summarize the recent archeogenomic reconstruction of population admixture in Europe and demonstrate that skin lightening happened as late as 5000 years ago through immigration of lighter pigmented populations from western Anatolia and the Russian steppe but not primarily via evolutionary pressure for vitamin D3 synthesis. We show that variations in genes encoding for proteins being responsible for the transport, metabolism and signalling of vitamin D provide alternative mechanisms of adaptation to a life in northern latitudes without suffering from consequences of vitamin D deficiency. This includes hypotheses explaining differences in the vitamin D status and response index of European populations.
Mesoscale diffusion magnetic resonance imaging of the ex vivo human hippocampus

Mesoscale diffusion magnetic resonance imaging (MRI) endeavors to bridge the gap between macroscopic white matter tractography and microscopic studies investigating the cytoarchitecture of human brain tissue. To ensure a robust measurement of diffusion at the mesoscale, acquisition parameters were arrayed to investigate their effects on scalar indices (mean, radial, axial diffusivity, and fractional anisotropy) and streamlines (i.e., graphical representation of axonal tracts) in hippocampal layers. A mesoscale resolution afforded segementation of the pyramidal cell layer (CA1‐4), the dentate gyrus, as well as stratum moleculare, radiatum, and oriens. Using ex vivo samples, surgically excised from patients with intractable epilepsy (n = 3), we found that shorter diffusion times (23.7 ms) with a b‐value of 4,000 s/mm2 were advantageous at the mesoscale, providing a compromise between mean diffusivity and fractional anisotropy measurements. Spatial resolution and sample orientation exerted a major effect on tractography, whereas the number of diffusion gradient encoding directions minimally affected scalar indices and streamline density. A sample temperature of 15°C provided a compromise between increasing signal‐to‐noise ratio and increasing the diffusion properties of the tissue. Optimization of the acquisition afforded a system's view of intra‐ and extra‐hippocampal connections. Tractography reflected histological boundaries of hippocampal layers. Individual layer connectivity was visualized, as well as streamlines emanating from individual sub‐fields. The perforant path, subiculum and angular bundle demonstrated extra‐hippocampal connections. Histology of the samples confirmed individual cell layers corresponding to ROIs defined on MR images. We anticipate that this ex vivo mesoscale imaging will yield novel insights into human hippocampal connectivity.
Macrophage migration inhibitory factor inhibits BMP-4 induced apoptosis

Non-canonical bone morphogenic protein (BMP) pathway signaling plays a critical role during embryonic neurogenesis, inducing apoptosis and eliminating an excess of neural progenitor cells, in preparation for the population of the neural stem cell niches. Our previous work discovered that non-canonical BMP signaling also induced the expression of the anti-apoptotic cytokine macrophage migration inhibitory factor (MIF). Because there are residual neural progenitors that escape BMP induced apoptosis, we believed the expression of MIF could be used to counter this specific type of developmental apoptosis. In vitro studies using P19 cells and ex vivo studies using E13 neural progenitor from wild type and mif-/-mice revealed that overexpression of mif was able to counteract BMP induced apoptosis, while in contrast ablation of mif resulted in a dramatic increase in apoptosis. Despite this finding, it is interesting to note that mif-/-mice, while presenting an overall increase in apoptosis are viable, ablation of mif expression in zebrafish and frog are embryonic lethal, suggesting a redundant or non-critical role of MIF in the developing mammalian embryo.
OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa).

Following double fertilization, plant endosperm nuclei undergo syncytial divisions, followed by synchronous cellularization. Cellularization is a key event during endosperm development, but our understanding of its regulation is limited to Arabidopsis. In this study we show that OsbZIP76 regulates cellularization in rice (Oryza sativa). Activation of OsbZIP76 coincided with the initiation of cellularization, and its knockdown or knockout mutants exhibited precocious cellularization. Genes involved in endosperm development or starch biosynthesis were prematurely activated in the osbzip76 caryopsis. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity; however, it interacted with the nuclear factor Y (NF-Y) family transcription factors OsNF-YB9 and OsNF-YB1 in yeast and in planta. OsbZIP76 and OsNF-YB9 were predominantly expressed in the endosperm and the proteins colocalized. Seeds of osnf-yb1 and osbzip76 mutants showed reduced size and reduced apparent amylose content. The parent-of-origin-dependent expression of OsbZIP76 is variable in different rice accessions. In summary, OsbZIP76 is an endosperm-expressed imprinted gene that regulates endosperm development in rice. This article is protected by copyright. All rights reserved.
ANTHELMINTIC ACTIVITY OF CASTOR OIL AND MUSTARD OIL

The aim of the present study was to investigate theÂ anthelminthicÂ activity of vegetable fixed oils, castor oil and mustard oil using adult earthworm, PheritimaÂ posthuma . The oils were tested at different concentrations for the determination of paralysis time and death time of the earthworms. Â Albendazole is used as standard and it was found that castor oil and mustard oil showed a better anthelminthic activity in comparison with the standard. Key words: AnthelminthicÂ activity,Â Albendazole, Earthworm, Castor oil, Mustard oil Sarvani Manthri et al. AnthelminticÂ Activity of Castor Oil and Mustard Oil. J Phytol 3/3 (2011) 12-14.