Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterosis for Grain Yield and Quality Traits in Maize (Zea mays L.)

Heterosis was estimated in 63 experimental hybrids obtained by crossing 9 productive inbred lines and 7 QPM (Quality protein miaze) inbred lines using line × tester mating design in maize. Sixty three hybrids along with 16 parents and two standard checks were evaluated for seventeen characters during Kharif 2014. Heterosis studies indicated the expression of standard heterosis and heterobeltiosis in several crosses for most of the characters in both desirable and undesirable direction. Over standard check, experimental hybrid HKI 1128 x HKI 163 manifested high heterotic effect for grain yield and other traits i.e plant height, ear height, number of cobs per plant, number of grains per cob over check 2 i.e HM 5 and for 100 grain weight over check 1 i.e HQPM 1, whereas, HKI 659-3 x HKI 194-6 showed highest standard heterosis for number of grains per cob, 100 grain weight and grain yield per plant indicating such experimental hybrids may be used for early maturing hybrids with high grain yield. The experimental hybrid HKI 1126 x HKI 161was found to exploit highest standard heterosis for phonological traits i.e days to 50 % taselling, days to 50 % silking, days to maturity (over HQPM 1) and grain yield per plant (over HM 5). HKI 488 x HKI 170(1+2) and HKI 659-3 x HKI 193-2 menifested high heterosis for both lysine and tryptophan content over HQPM 1as well as for protein content (over HM 5) and HKI 1040-4 x HKI 163 showed high heterosis for lysine content, tryptophan content and 100 grain weight over HQPM 1 as well as for number of grains per cob and grain yield per plant suggesting that these experimental hybrids can be used in QPM hybrid breeding programmes.
Effects of different potato cultivars on life history and demographic parameters of Phthorimaea operculella Zeller (Lepidoptera: Gelechiidae)

ABSTRACT Potato tuber worm, Phothorimae operculella Zeller (Lepidoptera: Gelechiidae) is a common pest of potato which causes a heavy loss in yield either in fields or storage. The effect of six potato cultivars (Agria, Florida, Impala, Picasso, Satina, and Sprint) were evaluated on the life history, life table and demographic parameters of P.operculella under laboratory conditions, which could be appropriate indices in resistance and susceptibility evaluation of potato cultivars. The longest development time was on Picasso (28.76 ± 0.36d) cultivar. The male longevity ranged from 4.83 ± 0.44d on Sprint to 7.45 ± 0.60d on Picasso. Impala and Satina with 53.22 ± 7.78 and 28.74 ± 3.54 eggs/individual had the highest and the lowest net reproductive rates (R0). The highest values for the intrinsic rate of increase (rm) and finite rate of increase (λ) were on Impala (rm: 0.119 day−1, λ: 1.75 day−1), and the lowest value was on Sprint (rm: 0.090 day−1, λ: 1.01 day−1). The results indicated that Sprint was the most resistant cultivar for the feeding of P.operculella, which could be useful in the development of integrated pest management programs for this pest.
Emergence of V1 connectivity pattern and Hebbian rule in a performance-optimized artificial neural network

The connectivity pattern and function of the recurrent connections in the primary visual cortex (V1) have been studied for a long time. But the underlying mechanism remains elusive. We hypothesize that the recurrent connectivity is a result of performance optimization in recognizing images. To test this idea, we added recurrent connections within the first convolutional layer in a standard convolutional neural network, mimicking the recurrent connections in the V1, then trained the network for image classification using the back-propagation algorithm. We found that the trained connectivity pattern was similar to those discovered in biological experiments. According to their connectivity, the neurons were categorized into simple and complex neurons. The recurrent synaptic weight between two simple neurons is determined by the inner product of their receptive fields, which is consistent with the Hebbian rule. Functionally, the recurrent connections linearly amplify the feedforward inputs to simple neurons and determine the properties of complex neurons. The agreement between the model results and biological findings suggests that it is possible to use deep learning to further our understanding of the connectome.
Biomass use and its health effects among the vulnerable and marginalized refugee families in the Gaza Strip

Introduction Biomass fuel remains the most common type of fuel used in many developing countries, leading to indoor air pollution and serious health impacts. Objective The objective of this study was to compile evidence on the impact household fuel combustion has on child and adult health, with an emphasis on solid fuel use in Gaza. Methods In this cross-sectional study, 110 structured self-administered questionnaires were distributed in April 2019 among families living in the Al-Maghazi refugee camp. Results Participants reported that the main fuel used were wood, coal, cardboard, and a mix of wood, cardboard, and plastic, which were used for cooking, heating, baking, boiling water, and lighting. The most common symptoms were nasal irritation (71.8%), followed by headache (66.4%) and dizziness (65.4%). The results of logistic regression showed that the participants who used wood fuel had a higher chance of feeling eye irritation than those who used a mix of wood, cardboard, and dried grass (OR = 1.316; 95% CI = 1.54–8.99). The participants who opened windows during the burning process of biomass fuel were five times more likely to develop pneumonia than those who closed windows (OR = 5.53; 95%CI = 11.60–19.0). Conclusion there is an urgent need for community awareness campaigns designed to inform people about the risks of exposure to biomass fuel smoke and how to better implement household ventilation.
Conserved redox‐dependent DNA binding of ROXY glutaredoxins with TGA transcription factors

Abstract The Arabidopsis thaliana CC‐type glutaredoxin (GRX) ROXY1 and the bZIP TGA transcription factor (TF) PERIANTHIA (PAN) interact in the nucleus and together regulate petal development. The CC‐type GRXs exist exclusively in land plants, and in contrast to the ubiquitously occurring CPYC and CGFS GRX classes, only the CC‐type GRXs expanded strongly during land plant evolution. Phylogenetic analyses show that TGA TFs evolved before the CC‐type GRXs in charophycean algae. MpROXY1/2 and MpTGA were isolated from the liverwort Marchantia polymorpha to analyze regulatory ROXY/TGA interactions in a basal land plant. Homologous and heterologous protein interaction studies demonstrate that nuclear ROXY/TGA interactions are conserved since the occurrence of CC‐type GRXs in bryophytes and mediated by a conserved ROXY C‐terminus. Redox EMSA analyses show a redox‐sensitive binding of MpTGA to the cis‐regulatory as‐1‐like element. Furthermore, we demonstrate that MpTGA binds together with MpROXY1/2 to this motif under reducing conditions, whereas this interaction is not observed under oxidizing conditions. Remarkably, heterologous complementation studies reveal a strongly conserved land plant ROXY activity, suggesting an ancestral role for CC‐type GRXs in modulating the activities of TGA TFs. Super‐resolution microscopy experiments detected a strong colocalization of ROXY1 with the active form of the RNA polymerase II in the nucleus. Together, these data shed new light on the function of ROXYs and TGA TFs and the evolution of redox‐sensitive transcription regulation processes, which likely contributed to adapt land plants to novel terrestrial habitats.
Bioinformatics analysis quantifies neighborhood preferences of cancer cells in Hodgkin lymphoma

Motivation Hodgkin lymphoma is a tumor of the lymphatic system and represents one of the most frequent lymphoma in the Western world. It is characterized by Hodgkin cells and Reed-Sternberg cells, which exhibit a broad morphological spectrum. The cells are visualized by immunohistochemical staining of tissue sections. In pathology, tissue images are mainly manually evaluated, relying on the expertise and experience of pathologists. Computational quantification methods become more and more essential to evaluate tissue images. In particular, the distribution of cancer cells is of great interest. Results Here, we systematically quantified and investigated cancer cell properties and their spatial neighborhood relations by applying statistical analyses to whole slide images of Hodgkin lymphoma and lymphadenitis, which describes a non-cancerous inflammation of the lymph node. We differentiated cells by their morphology and studied the spatial neighborhood relation of more than 400,000 immunohistochemically stained cells. We found that, according to their morphological features, the cells exhibited significant preferences for and aversions to cells of specific profiles as nearest neighbor. We quantified differences between Hodgkin lymphoma and lymphadenitis concerning the neighborhood relations of cells and the sizes of cells. The approach can easily be applied to other cancer types. Contact ina.koch@bioinformatik.uni-frankfurt.de
The characteristic time‐scale of perceived information for decision‐making: Departure from thermal columns in soaring birds

While climbing a warm risingair column (thermal), soaring birds need to balance too early departure (waste of climbing opportunity) against too late departure (waste of time with no further significant displacement), given the uncertainty about the thermal ahead. Such decisions that deal with where and when individuals move affect energy reservoirs and determine the accompanying costs of movement (Alerstam & Lindström, 1990; Nathan et al., 2008; Shepard et al., 2013). The use of passive soaring instead of selfpowered flight affects locomotion costs, as passive soaring costs 3–20 times less than selfpowered flight (Sapir, Wikelski, McCue, Pinshow, & Received: 2 October 2017 | Accepted: 28 March 2018 DOI: 10.1111/1365-2435.13136
The role of calnexin, calreticulin and heavy chain glycosylation in MHC class I assembly

﻿ Class I heavy chain (HC) must assemble with β-microglobulin (β2m) and acquire optimal peptide in order to be presented to cytotoxic T cells (CTLs). Calnexin is involved in the initial folding of class I HC and subsequent assembly with β2m. Incorporation of "empty" or suboptimally loaded class I molecules into the multimolecular loading complex is essential for them to acquire optimal peptides. The loading complex consists of several cofactors: TAP, tapasin, ERp57 and calreticulin. The precise role of calnexin and calreticulin in the regulated assembly and peptide loading and the significance of their physical interaction with other cofactors of the loading as well as preloading complex still remains unclear. Using mouse fibroblasts that lack calreticulin, I have studied the role of calreticulin in the assembly and loading of H2-K b and H2-D b expressed in these cells. MHC class I molecules in calreticulin-deficient cells are able to assemble with β2m normally, but their subsequent loading with optimal, stabilising peptides is defective despite their ability to interact with the TAP complex. The "empty" or suboptimally loaded class I molecules exit the ER rapidly. Reflecting the loading defect, presentation of endogenously processed antigens by class I molecules in calreticulin-deficient cells is impaired. I have used a human calnexin-deficient cell line CEM.NK R to study assembly of class I in the absence of calnexin. The results demonstrate that contrary to current understanding, calnexin has an important role in class I HC assembly with (32- microglobulin. The role of heavy chain glycosylation in class I biogenesis is still controversial. My findings suggest asparagine (N)-linked glycosylation of human class I heavy chain at position 86 is optimal and any deviations from "normal" glycosylation results in poor loading with peptides and some defect in the assembly with β2m. Despite affecting the loading function, glycosylation did not have significant effect on presentation of a high affinity binding epitope to HLA-A*0201 specific CTLs. Finally, I show that co-operation from all domains of calreticulin is essential in order to generate a fully functional calreticulin. Interestingly, proline-rich (P) -domain of calreticulin downregulated expression of a number of cellular proteins including MHC class I HC, despite restoring the cytosolic calcium levels in calreticulindeficient cells. The effect of P-domain on class I expression was at the level of transcription.
Study of oxidative stress in relation with antioxidant status in chronic bronchitis

Lipid peroxide plays an important role in inflammatory lung diseases. Increased epithelial permeability produced by cigarette smoke is likely to be mediated though depletion of the Total Antioxidant Capacity . Oxidative stress has been recognized as a central feature of smoke induced chronic bronchitis. Imbalance between oxidants and Total Anioxidant Capacity is also an established fact in these patients. 60 patients with chronic bronchitis included in the study. Their base line clinical examination, malondialdehyde (MDA), nitric oxide, alpha tochopherol and Total Antioxidant Capacity were measured. 100 healthy non-smokers’ were served as controls. The mean malondialdehyde levels and nitric oxide in the patients at base line were higher than Controls (p<0.001). Plasma alpha-tocopherol and total antioxidant capacity were lower (p<0.001) in the patients compared to controls. The present study shows that initially the plasma lipid peroxide (MDA) levels were high and antioxidants. (alpha- tocopherol, total antioxidant capacity) were low in patients with chronic bronchitis. Our results suggest the presence of oxidative stress and decrease in total antioxidant capacity in chronic bronchitis. DOI: http://dx.doi. org/10.11591/ijphs.v1i1. 523 Full Text: PDF
Molecular cytogenetics in different populations of Oligosarcus paranensis (Characidae): comparative analysis of the genus with 5S and 18S rDNA probes

Abstract Oligosarcus is a small genus of fish of the Characidae family and currently has 24 species widely distributed in Brazilian hydrographic systems. Cytogenetic studies were carried out in a few species of the genus, most of them from the Paraná river basin, as is the case of O. paranensis that exhibited interpopulational variations. In the present study, two populations of O. paranensis were analyzed cytogenetically in order to verify if the geographic distance between them generated some karyotypic alteration. Both populations exhibited 50 chromosomes and only two 5S rDNA sites. A marked variability in karyotype formulas, distribution of heterochromatic regions and 18S rDNA patterns were observed and their origin reflects the participation of different chromosomal rearrangements, which are considered the major events involved in the chromosome evolution of this group of fish.
Molecular Systematics of the Butterfly Tribe Baorini (Lepidoptera: Hesperiidae) from China

Abstract: The phylogenetic relationships of 16 species in 7 genera of butterflies belonging to the tribe Baorini in China were explored based on the partial sequences of three mitochondrial genes (Cytb, ND1 and 16S rDNA). Molecular phylogenetic trees were constructed using Maximum Likelihood (ML) and Bayesian Inference (BI) analyses. The monophyly of Baorini was confirmed with strong support. In addition, phylogenetic analyses suggest that Parnara, Baoris, Pelopidas and Caltoris are monophyletic. Baoris and Pelopidas are sister groups with strong support, whereas the relationships among Borbo, Pseudoborbo and Caltoris remain uncertain. A great differentiation was found between two subspecies of Parnara guttata, i.e., Pa. guttata guttata and Pa. guttata mangala in our molecular analysis results. Combined with their morphological differences, this leads us to suggest Pa. guttata mangala is an independent species.
Komposisi makanan dalam lambung teripang

Teripang merupakan salah satu kelas dari filum Echinodermata, dimana tubuh teripang bertekstur lunak, berdaging, berbentuk silindris memanjang seperti ketimun sehingga hewan ini sering disebut ketimun laut. Teripang merupakan organisme bentos yang cara makannya deposit feeding yaitu mengkonsumsi makanan yang tersimpan atau terdeposit dalam sedimen. Penelitian ini bertujuan untuk mengetahui komposisi jenis makanan dalam lambung teripang sehingga dapat diaplikasikan dalam usaha pemeliharaan teripang. Penelitian dilakukan dengan mengkoleksi sampel teripang secara bebas pada perairan intertidal Desa Suli pada bulan Maret 2014, kemudian dilanjutkan dengan mengidentifikasi jenis makanan dalam lambung teripang pada laboratorium biologi Universitas Darussalam Ambon pada bulan April 2014. Hasil penelitian terhadap 26 ekor teripang yang terdiri dari 6 jenis yaitu Holothuria scabra, Holothuria atra, Holothuria nobilis, Holothuria axiologa, Bohadschia marmorata dan Bohadcshia graeffei, ditemukan adanya komposisi makanan dalam lambung teripang yaitu fitoplankton dan zooplankton. Komposisi terbesar dalam lambung teripang adalah fitoplankton kelas Diatom/Baccilariophyceae sebesar 56% yang terdiri dari 23 genus.
INVITED EDITORIAL Statistical Approaches to Gene Mapping

In this brief primer, we hope to provide a general overview on statistical methods for disease-gene mapping. Of course, this cannot be complete—our apologies to researchers whose methods are not mentioned below. More-detailed information may be found in relevant textbooks (Ott 1999) and at the Web Resources of Genetic Linkage Analysis site (Laboratory of Statistical Genetics, Rockefeller University). The main purpose of this primer is to present, in a nontechnical manner, the methodological background and rationale of genetic mapping and to relate the various approaches to each other. In addition, current analysis methods for analysis of microarray data are discussed. Microarray data represent a new type of information that can provide important insight about the interaction of genes and that thus can complement the statistical approaches to gene mapping. Statistical genetic-mapping methods all rest on one biological phenomenon, recombination (crossing-over), which is exploited for the purposes of determining the genetic distance—or at least the closeness—between two loci. Crossovers between homologous chromosome strands occur semirandomly. Loci in close proximity to each other will rarely be separated by a recombination, whereas, for distant loci, recombinations occur as often as not. This phenomenon is used to derive a statistical measure of genetic distance. In family pedigrees, recombinations may be seen more or less directly; on the other hand, the consequences of recombinations in past generations can be observed in the form of linkage disequilibrium—that is, the preferential occurrence, in one gamete, of specific alleles at different loci.
Resource use and food preferences in understory ant communities along a complete elevational gradient in Papua New Guinea

Elevational gradients provide an interesting opportunity for studying the effect of climatic drivers over short distances on the various facets of biodiversity. It is globally assumed that the decrease in species richness with increasing elevation follows mainly the decrease in ecosystem productivity, but studies on functional diversity still remain limited. Here, we investigated how resource use and food preferences by both individual ant species and communities foraging in the understory vary with elevation along a complete elevational gradient (200 to 3200 m asl). Five bait types reflecting some of the main ecosystem processes in which ants are involved were tested: mutualism (sucrose and melezitose), predation (live termites), and detritivory (crushed insects and chicken feces). The observed monotonic decrease in both species richness and occurrences with elevation increase was accompanied by changes in some of the tested ecosystem processes. Such variations can be explained by resource availability and/or resource limitation: Predation and bird feces removal decreased with increasing elevation possibly reflecting a decline in species able to use these resources, while insect detritivory and nectarivory were most probably driven by resource limitation (or absence of limitation), as their relative use did not change along the gradient. Consequently, resource attractiveness (i.e., food preferences at the species level) appears as an important factor in driving community structuring in ants together with the abiotic environmental conditions.
Cerinichthys koelblae, gen. et sp. nov., from the Upper Jurassic of Cerin, France, and Its Phylogenetic Setting, Leading to a Reassessment of the Phylogenetic Relationships of Halecomorphi (Actinopterygii)

ABSTRACT Unknown, well-preserved fish specimens from the Upper Jurassic Plattenkalk of Cerin, France, found in the historical collection in Muséum d'Histoire Naturelle de Lyon, France, and from the excavation site of the Collections de Géologie, Université Claude Bernard Lyon 1, France, permit description of Cerinichthys koelblae, gen. et sp. nov. This new genus differs from all other Halecomorphi in the following combination of features: 27 caudal principal rays; 51 vertical scale rows; presence of broadened basal fin segments in the posterior rays of the pectoral, pelvic, anal, and dorsal fins and the median rays of the caudal fin; complete absence of vertebral centra in adult-sized individuals and multiple small scales in the median and ventral parts of the caudal peduncle. Investigations concerning the phylogenetic setting of the new genus Cerinichthys led to a proposal for a revision of the Halecomorphi, with Cerinichthys as a basal member of the new order Ophiopsiformes. The new family Ophiopsiellidae, as replacement for Ophiopsidae, within the Ophiopsiformes, are ganoinscaled Halecomorphi with one horizontally elongated dorsal fin or two dorsal fins. The Ionoscopidae are proposed to belong in the Amiiformes, and the order Ionoscopiformes needs to be reconsidered. The more basal Halecomorphi with massive ganoin scales remain poorly known, compared with the more advanced halecomorph group of the Amiidae. Closer investigation of their morphology and taxonomic relationships is therefore important for understanding broader patterns of halecomorph evolution.
EFFECT OF ORGANIC FERTILIZATION AND ACTIVE DRY YEAST ON PRODUCTIVITY OF THREE-LOBED SAGE (SALVIA FRUTICOSA MILL.) PLANTS UNDER SIWA OASIS CONDITIONS

per feddan. The sub-plots included foliar spray of active dry yeast concentrations of 0, 5 and 10 g /liter. The interaction effect proved that the highest compost manure level at 20 m 3 per feddan combined with foliar spray of the highest yeast concentration at 10 g/liter gave significantly maximum increments in vegetative growth parameters, yields of herb and essential oil as well as a higher 1,8-cineole constituent content in the volatile oil over control treatment, which recorded the lowest parameters.