Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi Activity QSAR Models for Anti- Parasite Drugs Using Markov Entropy Indices

There are many parasite species with very different antiparasite drugs susceptibility. Computational methods in biology and chemistry prediction of the biological activity based on Quantitative Structure-Activity Relationships (QSAR) susbtantialy increases the potentialities of this kind of networks avoiding time and resources consming experiments. Unfortunately, almost QSAR models are unspecific or predict activity against only one species. To solve this problem we developed here a multi-species QSAR classification model (ms-QSAR). In so doing, we use Markov Chains theory to calculate new multi-target spectral moments to fit a QSAR model that predict by the first time a ms-QSAR model for 500 drugs tested in the literature against 16 parasite species and other 207 drugs no tested in the literature using entropy type indices. The data was processed by Artificial Neural Network (ANN) classifying drugs as active or non-active against the different tested parasite species. The best ANN found was MLP 23:23-18-1:1. Overall model classification accuracy was 85.65% (211/244 cases) in training. Validation of the model was carried out by means of external predicting series. In this serie, the model classified correctly 81.85% (275/357 cases).
Mechanisms of Mitotic Spindle Disassembly and Positioning in Saccharomyces cerevisiae

When a cell divides, it must accurately replicate its genetic material and then faithfully segregate this material into the resulting daughter cells. My research addresses the latter half of this problem, focusing on how the cell regulates the function of the mitotic spindle, an elegant microtubule-based machine that attaches to replicated DNA and pulls it apart during mitosis. Here, I present two studies that investigate how the cell disassembles the mitotic spindle at the end of mitosis and how the cell positions the mitotic spindle prior to mitotic completion.I combined genetic analysis with live-cell fluorescence microscopy to identify the subprocesses driving spindle disassembly as well as the proteins that perform these subprocesses. Our results suggest that mechanistically distinct pathways largely governed by the anaphase-promoting complex, Aurora B kinase, and kinesin-8 cooperate to drive spindle disassembly in budding yeast. We also describe the roles of novel disassembly factors such as the spindle protein She1 and the 7-protein Alternative Replication Factor C complex. Together, these pathways disengage the mitotic spindle halves, inhibit spindle microtubule growth, and promote sustained spindle microtubule depolymerization. Strikingly, combined inhibition of pairs of disassembly pathways yielded cells with hyper-stable spindle remnants, which caused dramatic defects in cell cycle progression, thus establishing that regulated and rapid spindle disassembly is crucial for cell proliferation.To better understand the mechanisms of spindle positioning, I examined how the dynein-driven spindle-positioning pathway in budding yeast is silenced. My work suggests that dynein activity is regulated through interaction with the multi-subunit dynactin complex at anaphase and identifies a new cellular factor, She1, which controls this interaction. Dynactin is a well-known dynein activator, and, in budding yeast, the complete complex is required for dynein-dependent spindle movement. I found that localization of the dynactin complex is cell cycle-regulated, such that dynactin is recruited to astral microtubules, via interaction with dynein, primarily during anaphase. Additionally, we discovered that the protein She1 is a cell cycle-regulated inhibitor of dynein activity. Without She1, dynein activity extends beyond anaphase and, as a result, mis-positions the mitotic spindle. Strikingly, loss of She1 also permits recruitment of the dynactin complex to astral microtubules throughout the cell cycle. These results suggest that in wild-type cells, She1 restricts dynein activity to anaphase by preventing the interaction between dynein and the complete dynactin complex.
Is There Any Relationship between Upper and Lower Limb Impairments in People with Multiple Sclerosis? A Kinematic Quantitative Analysis

Background In people with multiple sclerosis (pwMS), disability is generally assessed on the basis of ambulation abilities, whereas upper limb motor dysfunctions are less frequently considered. Nevertheless, they can severely affect the quality of life of pwMS. To date, it remains mostly unknown whether a relationship exists between upper and lower limb impairments. Aim To investigate the existence of a relationship between upper and lower limb impairments in pwMS based on two fundamental motor tasks, namely walking and hand-to-mouth (HTM) movement. Methods Twenty-eight pwMS with Expanded Disability Status Scale (EDSS) scores in the range of 1–6, and 21 healthy controls (HC) underwent a kinematic analysis of gait and HTM movement performed with a motion capture system. The spatiotemporal parameters for the two tasks were calculated and correlated using Spearman's rank correlation coefficients. Results The pwMS performed worse than HC on both tasks. Small to large correlations were found between the total HTM movement duration and most of the gait parameters (rho, 0.35–0.68; p < 0.05). Conclusions Both upper and lower limb motor abilities in pwMS worsen as disability increases. Nevertheless, their relationship is only moderate. This finding emphasizes the need for specific tests to quantify disability considering the overall motor function in pwMS.
Effects of Dietary Zeolite Supplementation as an Antibiotic Alternative on Growth Performance, Intestinal Integrity, and Cecal Antibiotic Resistance Genes Abundances of Broilers

Simple Summary The widespread use of antibiotics in livestock production has attracted public attention due to antibiotic resistance. It is necessary to search for antibiotic alternatives in feeds. Zeolite, a kind of feed additive or feed raw material, can enhance growth performance, balance intestinal bacteria, and improve antioxidant capacity in animals. In vitro studies showed zeolite could reduce antibiotic resistance genes (ARGs) abundances. This research compared the effects of antibiotics and zeolite on growth performance, intestinal morphology and barrier function, and cecal ARGs abundances of broilers. Our results indicated that dietary zeolite supplementation exerted similar or better effects than antibiotic inclusion. Abstract The study investigated the effects of dietary zeolite supplementation as an antibiotic alternative on growth performance, intestinal integrity, and cecal antibiotic resistance genes abundances of broilers. One-day-old chicks were assigned into three groups and fed a basal diet or a basal diet supplemented with antibiotics (50 mg/kg) or zeolite (10 g/kg). Antibiotic or zeolite increased (p < 0.05) average daily gain (ADG) from 1 to 42 days and duodenal villus height to crypt depth ratio (VH:CD) at 21 days. Zeolite increased (p < 0.05) ADG and average daily feed intake from 1 to 21 days, jejunal VH:CD at 21 and 42 days, ileal VH and VH:CD at 42 days, zonula occludens-1 mRNA abundance at 21 days, and duodenal occludin mRNA abundance at 42 days, whereas reduced (p < 0.05) jejunal CD and malondialdehyde levels in ileum at 21 days and duodenum at 42 days, serum D-lactic acid and diamine oxidase levels at 42 days, and plasma lipopolysaccharide content at 21 and 42 days. Antibiotics reduced (p < 0.05) duodenal claudin-2 mRNA abundance at 21 days, whereas increased (p < 0.05) cecal tetB abundance at 42 days. These findings suggested that the beneficial effects of zeolite in broilers were more pronounced than that of antibiotics.
The Relation of Optimism to Relative Telomere Length in Older Men and Women.

OBJECTIVE Mounting evidence suggests that higher optimism is associated with reduced risk of age-related morbidities and premature mortality. Yet, possible biological mechanisms underlying these associations remain understudied. One hypothesized mechanism is a slower rate of cellular aging, which in turn delays age-related declines in health. METHODS We used data from two large cohort studies to test the hypothesis that higher optimism is associated with longer leukocyte telomere length. Using cross-sectional data from the Health and Retirement Study (HRS; N=6,417; mean age=70 years) and the Women's Health Initiative (WHI; N=3,582; mean age=63 years), we used linear regression models to examine the association of optimism with relative telomere length (assessed in leukocytes from saliva [HRS] or plasma [WHI]). Models adjusted for sociodemographics, depression, health status, and health behaviors. RESULTS Considering both optimism and telomere length as continuous variables, we found consistently null associations in both cohorts, regardless of which covariates were included in the models. In models adjusting for demographics, depression, co-morbidities, and health behaviors, optimism was not associated with mean relative telomere length (HRS: β=-0.002; 95% CI:-0.014, 0.011; WHI: β=-0.004; 95% CI:-0.017, 0.009). CONCLUSIONS Findings do not support mean telomere length as a mechanism that explains observed relations of optimism with reduced risk of chronic disease in older adults. Future research is needed to evaluate other potential biological markers and pathways.
EXPRESSION OF HUMAN LEUKOCYTE ANTIGEN-E AND NATURAL KILLER CELLS IN INTRA UTERINE FETAL DEATH

Intra Uterine Fetal Death (IUFD) is one contributor to infant mortality. Human Leukocyte Antigen-E (HLA-E) and Natural Killer Cells (NK cells) are believed to play an important role towards IUFD associated with immune maladaptation. This study aimed to determine the expression of HLA-E and NK cells on trophoblast on IUFD and normal pregnancy. The study used cross sectional approach undertaken at Department of Obstetrics and Gynecology, Dr. Moewardi Hospital, Surakarta, networking hospitals, and Anatomic Pathology Laboratory of Faculty of Medicine, Sebelas Maret University. The number of samples were 32 subjects consisting of 16 subjects with normal pregnancy and 16 subjects with IUFD. The expression of HLA-E and NK cells on trophoblast of subjects who met the inclusion and exclusion criteria were examined using immunohistochemistry method and t-test statistical analysis. The mean value of HLA-E expression in the trophoblast of IUFD group was 17.30±6.69, in normal pregnancy was 57.06±32.04, with p=0.00 (p<0.05). The mean value of NK cell expression in trophoblast in IUFD group was 78.62±36.43, in normal pregnancy was 19.87±6.43, with p=0.00 (p<0.05). This study concluded that the expression of HLA-E was lower and NK cells wass higher in IUFD compared to those in normal pregnancy.
C V ] 1 4 D ec 2 01 7 Emotion Classification with Data Augmentation Using Generative Adversarial Networks

It is a difficult task to classify images with multiple class labels using only a small number of labeled examples, especially when the label (class) distribution is imbalanced. Emotion classification is such an example of imbalanced label distribution, because some classes of emotions like disgusted are relatively rare comparing to other labels like happy or sad. In this paper, we propose a data augmentation method using generative adversarial networks (GAN). It can complement and complete the data manifold and find better margins between neighboring classes. Specifically, we design a framework using a CNN model as the classifier and a cycle-consistent adversarial networks (CycleGAN) as the generator. In order to avoid gradient vanishing problem, we employ the least-squared loss as adversarial loss. We also propose several evaluation methods on three benchmark datasets to validate GAN’s performance. Empirical results show that we can obtain 5%∼10% increase in the classification accuracy after employing the GAN-based data augmentation techniques.
Inferring Invasion Paths Into Cotton by Creontiades dilutus (Hemiptera: Miridae) From Arid Zone and Agricultural Sources

Abstract Managing agricultural pests that use multiple host plant species is a challenge when individuals move between host plants in natural vegetation and agricultural environments. The green mirid (Creontiades dilutus) Stål (Hemiptera: Miridae) is endemic to Australia and routinely invades cotton from local uncultivated vegetation, but may also originate from remote locations in the arid continental interior. This bug is polyphagous and highly mobile, which contributes to its pest status in cotton L. (Malvaceae) systems as well as its persistence in arid environments with sparsely distributed ephemeral host plants. The aim of this study was to evaluate how C. dilutus individuals use a variety of host species across remote arid regions and highly managed agricultural landscapes. Structured field surveys spanning vast areas across the Simpson Desert in the arid heart of Australia, as well as subcoastal cotton production systems, were designed to evaluate host use across environments that share few plant species. High numbers of C. dilutus were collected from Cullen australasicum (Schltdl.) J.W. Grimes (Fabaceae) (perennial hosts) and Goodenia cycloptera R.Br. (Goodeniaceae) (ephemeral hosts) in the desert following rain. In agricultural environments, C. dilutus bugs were mostly found on irrigated Medicago sativa L. (Fabaceae) (lucerne), and to a lesser extent Melilotus indicus (L.) All. (Fabaceae) near rivers. Significantly, bugs were on these plants prior to the planting of cotton across all environments surveyed. These data allow inferences relating host use, host abundance, and insect migration to one another to understand the connection that C. dilutus bugs have between arid and agricultural environments.
Tail expansions for random record distributions

The random record distribution ν associated with a probability distribution μ can be written as a convolution series, ν = [sum ]∞n=1n−1 (n + 1)−1μ*n. Various authors have obtained results on the behaviour of the tails ν((x, ∞)) as x → ∞, using Laplace transforms and the associated Abelian and Tauberian theorems. Here we use Gelfand transforms and the Wiener–Lévy–Gelfand Theorem to obtain expansions of the tails under moment conditions on μ. The results differ notably from those known for other convolution series.
CRISPR-Cas9–mediated therapeutic editing of Rpe65 ameliorates the disease phenotypes in a mouse model of Leber congenital amaurosis

Therapeutic genome editing of a nonsense mutation showed functional gain in a mouse model of inherited retinal degeneration. Leber congenital amaurosis (LCA), one of the leading causes of childhood-onset blindness, is caused by autosomal recessive mutations in several genes including RPE65. In this study, we performed CRISPR-Cas9–mediated therapeutic correction of a disease-associated nonsense mutation in Rpe65 in rd12 mice, a model of human LCA. Subretinal injection of adeno-associated virus carrying CRISPR-Cas9 and donor DNA resulted in >1% homology-directed repair and ~1.6% deletion of the pathogenic stop codon in Rpe65 in retinal pigment epithelial tissues of rd12 mice. The a- and b-waves of electroretinograms were recovered to levels up to 21.2 ± 4.1% and 39.8 ± 3.2% of their wild-type mice counterparts upon bright stimuli after dark adaptation 7 months after injection. There was no definite evidence of histologic perturbation or tumorigenesis during 7 months of observation. Collectively, we present the first therapeutic correction of an Rpe65 nonsense mutation using CRISPR-Cas9, providing new insight for developing therapeutics for LCA.
Optical coherence tomography angiography findings of the fellow eye of patients with unilateral neovascular age-related macular degeneration OCT-A Evaluation of Fellow Eyes of CNV

Purpose. Age related macular degeneration (ARMD) remains a serious cause of vision loss in elderly people worldwide. The purpose of the study is to investigate the fellow eye of the patients with exudative ARMD using optical coherence tomography angiography (OCTA). Methods. We conducted a retrospective study from the data of patients with exudative ARMD. Patients undergoing intravitreal anti-VEGF treatment for one eye were selected. OCTA images of both eyes with choroidal neovascularization (CNV) and the fellow eyes were evaluated retrospectively. Midchoroid, choriocapillaris (CC), retina pigment epithelium (RPE), and outer retina levels were evaluated using RTVue XR AVANTI OCTA. Results. There were 5 male and 5 female patients included in this study. We detected drusen and pigment epithelial detachments (PED) in fellow eyes. Six fellow eyes had vascularized PED. Four of them were acute flat irregular type; two of them were chronic dome shaped type. Four patients had soft drusen that had shown signal loss on choriocapillaris level. Conclusion. The follow-up of both eyes of the patients with ARMD is very important. OCTA seems a promising non-invasive method in order to detect subclinical early stage CNV and distinguish among types of PEDs.
The emergence of subclade A1 and A3 Avipoxviruses in India.

During the years 2010-2018, Avipoxvirus (APV) outbreaks were observed in the domestic chickens and pigeons present in the Eastern Indian state of Odisha. Based on typical pox lesions, followed by molecular techniques, the overall morbidity was found to be 18-19.23% and 16.92-23% in chickens and pigeons, respectively. The cutaneous forms of the disease were observed with varied rates of mortality, being 47.36-52.77% in chickens and 39.13-92% in pigeons. PCR amplification targeting the viral P4b core protein-coding gene and the DNA polymerase gene confirmed the presence of APV strains in 10 birds. Subsequent phylogenetic analysis of these two genes confirmed that the circulating strains were members of APV clade A. The subclade analysis revealed the introduction of A1 and A3 subclades in Indian chickens and pigeons, respectively. This study is the first molecular record of APVs circulating in Eastern Indian birds (Odisha) and involves the first use of the polymerase gene to reveal the circulating clades of Indian APVs.
DFPE: Explaining Predictive Models for Disk Failure Prediction

Recent research works on disk failure prediction achieve a high detection rate and a low false alarm rate with complex models at the cost of explainability. The lack of explainability is likely to hide bias or overfitting in the models, resulting in bad performance in real-world applications. To address the problem, we propose a new explanation method DFPE designed for disk failure prediction to explain failure predictions made by a model and infer prediction rules learned by a model. DFPE explains failure predictions by performing a series of replacement tests to find out the failure causes while it explains models by aggregating explanations for the failure predictions. A presented use case on a real-world dataset shows that compared to current explanation methods, DFPE can explain more about failure predictions and models with more accuracy. Thus it helps to target and handle the hidden bias and overfitting, measures feature importances from a new perspective and enables intelligent failure handling.
Genomic dissection of an extended phenotype: Oak galling by a cynipid gall wasp

Galls are plant tissues whose development is induced by another organism for the inducer's benefit. 30,000 arthropod species induce galls, and in most cases the inducing effectors and target plant systems are unknown. Cynipid gall wasps are a speciose monophyletic radiation that induce structurally complex galls on oaks and other plants. We used a model system comprising the gall wasp Biorhiza pallida and the oak Quercus robur to characterise inducer and host plant gene expression at defined stages through the development of galled and ungalled plant tissues, and tested alternative hypotheses for the origin and type of galling effectors and plant metabolic pathways involved. Oak gene expression patterns diverged markedly during development of galled and normal buds. Young galls showed elevated expression of oak genes similar to legume root nodule Nod factor-induced early nodulin (ENOD) genes and developmental parallels with oak buds. In contrast, mature galls showed substantially different patterns of gene expression to mature leaves. While most oak transcripts could be functionally annotated, many gall wasp transcripts of interest were novel. We found no evidence in the gall wasp for involvement of third-party symbionts in gall induction, for effector delivery using virus-like-particles, or for gallwasp expression of genes coding for plant hormones. Many differentially and highly expressed genes in young larvae encoded secretory peptides, which we hypothesise are effector proteins exported to plant tissues. Specifically, we propose that host arabinogalactan proteins and gall wasp chitinases interact in young galls to generate a somatic embryogenesis-like process in oak tissues surrounding the gall wasp larvae. Gall wasp larvae also expressed genes encoding multiple plant cell wall degrading enzymes (PCWDEs). These have functional orthologues in other gall inducing cynipids but not in figitid parasitoid sister groups, suggesting that they may be evolutionary innovations associated with cynipid gall induction.
Effect of Canopy Structure on Water Use of Wheat (Triticum Aestivum L.) During Post-Anthesis Stage

Abstract Wheat, being the main crop in Mediterranean type environments, is grown during winter under rainfed conditions and its yield potential is mostly affected by the amount and distribution of rain. This study is conducted at experimental fields of Ege University, Department of Field Crops in Izmir-Bornova which is characterized as Mediterranean type climate conditions during 2011/2012 and 2012/2013 growing season. Totally 9 canopy structures were generated by different row and line distances. Plant height, total dry weight, tiller number, harvest index, spike number, grain number per spike, thousand grain weight and grain yield were determined after harvest time while digital leaf area index and soil moisture contents were monitoring during specific growth periods to evaluate changes in soil water status by different canopy closer. Increasing in sowing density by different row and in-line distance reduced tiller and spike number per plant. On the other hand, grain number per spike and thousand grain weights were significantly affected by in-line distance instead of row distance. Higher grain yield were obtained from 20x1 cm treatments. Canopy cover speed determined using with digital imaging was not remarkable correlated (r=0.06) with soil moisture content during post-anthesis stage of wheat when higher rain amount is recorded in 2012. However, there was a significant negative correlation (r=0.51) between canopy cover speed and soil water status during post-anthesis stage when the rain amount is limited in 2013. We may suggest that rapid canopy cover lead to negative effect on soil water status via higher transpiration if the rain is limited during post-anthesis stage of wheat.