Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of diet and early quantitative feed restriction on the minimum weight requirement for onset of sexual maturity in white rock broiler breeders.

The effect of diet and feed restriction on minimum weight for onset of sexual maturity was studied in White Rock broiler breeders. In the restriction experiment, three groups of birds were subjected to moderate, severe, and very severe quantitative food restriction during the rearing period (19 week target weights: 1900, 1300, and 700 g, respectively). From 20 to 24 weeks body weight was equalized at 2200 g, and from 24 weeks birds were allowed to gain about 150 g/week until first egg. In the diet experiment, two groups of birds were raised under severe quantitative food restriction during the rearing period and then allowed to gain about 150 g/week on a low metabolizable energy/protein (ME/P) ratio diet (25.4% protein, ME/P = 116) and on a high ME/P ratio (14.7% protein, ME/P = 219) until first egg. All birds were killed at first egg. Birds of the three restriction groups entered lay at the same lean body weight and ash and protein content, but at different age, carcass weight, shank length, dry matter, and fat content. Birds of the two diet groups entered lay at the same lean body weight, shank length, and ash content but at different carcass weight, dry matter, and fat content. Considering both experiments together, birds of the different treatment groups entered lay at similar lean body weight and ash content but differed in age, carcass weight, shank length, dry matter, and fat content. (ABSTRACT TRUNCATED AT 250 WORDS)
A Meta-Analysis of Longitudinal Associations Between Substance Use and Interpersonal Attachment Security

Substance use has long been associated with close relationship distress. Although the direction of influence for this association has not been established, it has often been assumed that substance use is the causal agent and that close relationship distress is the effect. But research seeking to establish temporal precedence in this link has produced mixed findings. Further, theoretical models of substance use and close relationship processes present the plausibility of the inverse pathway—that insecure close relationships may serve as a vulnerability factor for the development of later substance problems. The current review applies an attachment-theoretical framework to the association between close social bonds and substance use and substance-related problems. Targeting longitudinal studies of attachment and substance use, we examined 665 effect sizes drawn from 34 samples (total N = 56,721) spanning time frames ranging from 1 month to 20 years (M = 3.8 years). Results revealed a significant prospective correlation between earlier attachment and later substance use (r = −.11, 95% CI [−.14, −0.08]). Further, cross-lagged coefficients were calculated which parsed auto-regressive effects, indicating that lower attachment security temporally preceded increases in substance use (r = −.05, 95% CI [−.06, −.04]). Analyses further indicated that the pathway from earlier attachment to later substance use was significantly stronger than that from earlier substance use to later attachment. Results also revealed several moderators of the attachment-substance use link. These findings suggest that insecure attachment may be a vulnerability factor for substance use, and indicate close relationship quality as a promising line of inquiry in research on substance use disorder risk.
T Tauri Stars Associated with Herbig-Haro Objects and Jets

We have obtained deep [S II] λλ6716, 6731 and continuum images of the five classical T Tauri stars (CTTSs) DP Tau, RW Aur, V536 Aql, LkHα 321, and V1331 Cyg. These CTTSs were selected for our imaging study because they either showed strong P Cygni absorptions in their spectra (LkHα 321, V1331 Cyg) or were known from long-slit spectroscopic studies to have bipolar jetlike outflows (DP Tau, RW Aur, V536 Aql). For the latter three objects, the spatial extent and structure of the outflows are studied here for the first time. In addition, LkHα 321 and V1331 Cyg were found to be associated with Herbig-Haro (HH) objects and/or HH jets. In four cases, the jets or outflows are bipolar, with the largest spatial extent seen in RW Aur (145″; 0.1 pc for d = 150 pc) and V1331 Cyg (360″; 1 pc for d = 550 pc). About 170″ west of LkHα 321, we have serendipitously discovered a faint HH source, which we designate LkHα 321B.
Fast Influence Maximization in Dynamic Graphs: A Local Updating Approach

We propose a generalized framework for influence maximization in large-scale, time evolving networks. Many real-life influence graphs such as social networks, telephone networks, and IP traffic data exhibit dynamic characteristics, e.g., the underlying structure and communication patterns evolve with time. Correspondingly, we develop a dynamic framework for the influence maximization problem, where we perform effective local updates to quickly adjust the top-k influencers, as the structure and communication patterns in the network change. We design a novel N-Family approach (N=1, 2, 3, .) based on the maximum influence arborescence (MIA) propagation model with approximation guarantee of (1-1/e). We then develop heuristic algorithms by extending the N-Family approach to other information propagation models (e.g., independent cascade, linear threshold) and influence maximization algorithms (e.g., CELF, reverse reachable sketch). Based on a detailed empirical analysis over several real-world, dynamic, and large-scale networks, we find that our proposed solution, N-Family improves the updating time of the top-k influencers by 1-2 orders of magnitude, compared to state-of-the-art algorithms, while ensuring similar memory usage and influence spreads.
Improving ecosystem service frameworks to address wicked problems

Complex problems often result from the multiple interactions between human activities and ecosystems. The interconnected nature of ecological and social systems should be considered if these “wicked problems” are to be addressed. Ecosystem service approaches provide an opportunity to link ecosystem function with social values, but in practice the essential role that social dynamics play in the delivery of outcomes remains largely unexplored. Social factors such as management regimes, power relationships, skills, and values, can dramatically affect the definition and delivery of ecosystem services. Input from a diverse group of stakeholders improves the capacity of ecosystem service approaches to address wicked problems by acknowledging diverse sets of values and accounting for conflicting world views. Participatory modeling can incorporate both social and ecological dynamics into decision making that involves stakeholders, but is itself a complex social undertaking that may not yield precise or predictable outcomes. We explore the efficacy of different types of participatory modeling in relation to the integration of social values into ecosystem services frameworks and the generation of four important elements of social capital needed to address wicked problems: enhancing social learning and capacity building; increasing transparency; mediating power; and building trust. Our findings indicate that mediated modeling, group mapping, and mental/conceptual modeling are likely to generate elements of social capital that can improve ecosystem service frameworks. Participatory simulation, system dynamic modeling, and Bayesian belief networks, if utilized in isolation, were found to have a low likelihood of generating the social capital needed to improve ecosystem services frameworks. Scenario planning, companion modeling, group model building, and participatory mapping all generate a moderate to high level of social capital elements that improve the capacity of ecosystem service frameworks to address wicked problems.
Tissue-specific Role of CX3CR1 Expressing Immune Cells and Their Relationships with Human Disease

Chemokine (C-X3-C motif) ligand 1 (CX3CL1, also known as fractalkine) and its receptor chemokine (C-X3-C motif) receptor 1 (CX3CR1) are widely expressed in immune cells and non-immune cells throughout organisms. However, their expression is mostly cell type-specific in each tissue. CX3CR1 expression can be found in monocytes, macrophages, dendritic cells, T cells, and natural killer (NK) cells. Interaction between CX3CL1 and CX3CR1 can mediate chemotaxis of immune cells according to concentration gradient of ligands. CX3CR1 expressing immune cells have a main role in either pro-inflammatory or anti-inflammatory response depending on environmental condition. In a given tissue such as bone marrow, brain, lung, liver, gut, and cancer, CX3CR1 expressing cells can maintain tissue homeostasis. Under pathologic conditions, however, CX3CR1 expressing cells can play a critical role in disease pathogenesis. Here, we discuss recent progresses of CX3CL1/CX3CR1 in major tissues and their relationships with human diseases.
Immune Monitoring of Cancer Patients Prior to and During CTLA-4 or PD-1/PD-L1 Inhibitor Treatment

Targeting the immune checkpoint receptors cytotoxic T lymphocyte antigen 4 (CTLA-4), programmed cell death protein 1 (PD-1), or programmed cell death 1 ligand 1 (PD-L1) represents a very attractive treatment modality for tumor patients. The administration of antibodies against these receptors can promote efficient antitumor effects and can induce objective clinical responses in about 20–40% patients with various tumor types, accompanied by improved survival. Based on their therapeutic efficiency, several antibodies have been approved for the treatment of tumor patients. However, many patients do not respond to checkpoint inhibitor therapy. Therefore, the identification of biomarkers is required to guide patient selection for this treatment modality. Here, we summarize recent studies investigating the PD-L1 expression or mutational load of tumor tissues as well as the frequency and phenotype of immune cells in tumor patients prior to and during CTLA-4 or PD-1/PD-L1 inhibitor treatment.
Grower diets and bird density effects on growth and cannibalism in ring-necked pheasants.

The effects of bird density and dietary protein and energy level on growth rate and feather pecking in Ring-Necked pheasants were investigated in two experiments. After brooding, pheasants in Experiment 1 were housed at densities of . 19, . 38, or . 74 m2/bird and fed grower diets containing 16, 19, or 22% protein. Experiment 2 pheasants were housed at . 4 m2/bird and fed diets containing 16 or 22% protein with energy levels of 2530, 2750, 2970, or 3190 kcal/kg. Body weight was not affected by bird density differences, but feather pecking was significantly reduced by increasing floor space per bird. Body weight, cannibalism, and feed conversion were poorer in groups fed the 16% protein diet than those fed the 19 or 22% protein diets. Body weight gains, feed efficiency, and feather pecking scores improved as the energy content of grower diets increased. Significant interactions existed between dietary protein and bird density and between dietary protein and energy for feather picking in pheasants. Total performance was best for groups fed a grower diet of 22% protein and 2970 kcal/kg metabolizable energy level with a floor space of . 38 m2 or greater per bird.
Asymmetric Modification of Hepatitis B Virus (HBV) Genomes by an Endogenous Cytidine Deaminase inside HBV Cores Informs a Model of Reverse Transcription

ABSTRACT Cytidine deaminases inhibit replication of a broad range of DNA viruses by deaminating cytidines on single-stranded DNA (ssDNA) to generate uracil. While several lines of evidence have revealed hepatitis B virus (HBV) genome editing by deamination, it is still unclear which nucleic acid intermediate of HBV is modified. Hepatitis B virus has a relaxed circular double-stranded DNA (rcDNA) genome that is reverse transcribed within virus cores from a RNA template. The HBV genome also persists as covalently closed circular DNA (cccDNA) in the nucleus of an infected cell. In the present study, we found that in HBV-producing HepAD38 and HepG2.2. 15 cell lines, endogenous cytidine deaminases edited 10 to 25% of HBV rcDNA genomes, asymmetrically with almost all mutations on the 5′ half of the minus strand. This region corresponds to the last half of the minus strand to be protected by plus-strand synthesis. Within this half of the genome, the number of mutations peaks in the middle. Overexpressed APOBEC3A and APOBEC3G could be packaged in HBV capsids but did not change the amount or distribution of mutations. We found no deamination on pregenomic RNA (pgRNA), indicating that an intact genome is encapsidated and deaminated during or after reverse transcription. The deamination pattern suggests a model of rcDNA synthesis in which pgRNA and then newly synthesized minus-sense single-stranded DNA are protected from deaminase by interaction with the virus capsid; during plus-strand synthesis, when enough dsDNA has been synthesized to displace the remaining minus strand from the capsid surface, the single-stranded DNA becomes deaminase sensitive. IMPORTANCE Host-induced mutation of the HBV genome by APOBEC proteins may be a path to clearing the virus. We examined cytidine-to-thymidine mutations in the genomes of HBV particles grown in the presence or absence of overexpressed APOBEC proteins. We found that genomes were subjected to deamination activity during reverse transcription, which takes place within the virus capsid. These observations provide a direct insight into the mechanics of reverse transcription, suggesting that newly synthesized dsDNA displaces ssDNA from the capsid walls, making the ssDNA accessible to deaminase activity.
Missing value imputation for gene expression data by tailored nearest neighbors

Abstract High dimensional data like gene expression and RNA-sequences often contain missing values. The subsequent analysis and results based on these incomplete data can suffer strongly from the presence of these missing values. Several approaches to imputation of missing values in gene expression data have been developed but the task is difficult due to the high dimensionality (number of genes) of the data. Here an imputation procedure is proposed that uses weighted nearest neighbors. Instead of using nearest neighbors defined by a distance that includes all genes the distance is computed for genes that are apt to contribute to the accuracy of imputed values. The method aims at avoiding the curse of dimensionality, which typically occurs if local methods as nearest neighbors are applied in high dimensional settings. The proposed weighted nearest neighbors algorithm is compared to existing missing value imputation techniques like mean imputation, KNNimpute and the recently proposed imputation by random forests. We use RNA-sequence and microarray data from studies on human cancer to compare the performance of the methods. The results from simulations as well as real studies show that the weighted distance procedure can successfully handle missing values for high dimensional data structures where the number of predictors is larger than the number of samples. The method typically outperforms the considered competitors.
alpha-tocopherol, beta-carotene, and retinol enrichment of chicken eggs.

Due to the numerous health benefits associated with consumption of antioxidants such as alpha-tocopherol and beta-carotene, an experiment was conducted to determine dietary levels that would significantly enhance their concentration in chicken egg yolks. In the experiment, 127 Single Comb White Leghorn laying hens were divided into treatment groups (n = 40 per treatment group) and fed diets containing 0, 50, 100, 200, or 400 mg/kg beta-carotene, dl-alpha-tocopheryl acetate, or their combination. Yolk alpha-tocopherol increased (P < .05) from the control level of 144 micrograms/g of yolk to 477 micrograms/g of yolk when 400 mg dl-alpha-tocopheryl acetate/kg of diet was supplemented. Yolk retinol levels increased (P < .05) from 11.6 micrograms/g of yolk in controls to 13.9 micrograms/g of yolk at 200 mg beta-carotene/kg of diet. beta-Carotene content in the yolk also increased (P < .05) from . 14 micrograms/g of yolk in controls to 5.19 micrograms/g of yolk at 200 mg beta-carotene/kg of diet. Supplemental beta-carotene markedly decreased the yolk deposition of alpha-tocopherol when the two compounds were fed together. Egg production, egg weight, and egg yield were not affected by dietary supplementations. Although the data indicated that it is possible to significantly increase the concentration of all three compounds in chicken eggs, because of the relative expense involved it may not be commercially viable to increase egg yolk concentrations of beta-carotene or retinol by supplementing beta-carotene in the diet.
Optimized Treatment Schedules for Chronic Myeloid Leukemia

Over the past decade, several targeted therapies (e.g. imatinib, dasatinib, nilotinib) have been developed to treat Chronic Myeloid Leukemia (CML). Despite an initial response to therapy, drug resistance remains a problem for some CML patients. Recent studies have shown that resistance mutations that preexist treatment can be detected in a substantial number of patients, and that this may be associated with eventual treatment failure. One proposed method to extend treatment efficacy is to use a combination of multiple targeted therapies. However, the design of such combination therapies (timing, sequence, etc.) remains an open challenge. In this work we mathematically model the dynamics of CML response to combination therapy and analyze the impact of combination treatment schedules on treatment efficacy in patients with preexisting resistance. We then propose an optimization problem to find the best schedule of multiple therapies based on the evolution of CML according to our ordinary differential equation model. This resulting optimization problem is nontrivial due to the presence of ordinary different equation constraints and integer variables. Our model also incorporates drug toxicity constraints by tracking the dynamics of patient neutrophil counts in response to therapy. We determine optimal combination strategies that maximize time until treatment failure on hypothetical patients, using parameters estimated from clinical data in the literature.
Nonlinear Hierarchical Control for Unmanned Quadrotor Transportation Systems

An unmanned quadrotor presents excellent mobility to fly freely in complex environments, which makes it an ideal choice for aerial transferring tasks. During the transferring process, it is very challenging to eliminate the swing, since there is no direct control on the payload. The quadrotor transportation system presents the great challenge of the cascaded underactuated–underactuated property, which makes it extremely difficult to simultaneously implement accurate quadrotor positioning and efficient payload swing suppression. In this paper, a nonlinear hierarchical control scheme is proposed for a quadrotor transportation system, which takes full advantage of the cascade property of the system and separates the controller design for the inner loop and the outer loop, respectively, to facilitate the design procedure. More specifically, for the outer loop subsystem, based on the proposed energy storage function, a virtual control vector is designed, which introduces a saturation function to make the desired attitude free of any singularities. For the inner loop, a coordinate-free geometric attitude tracking controller is designed on the Lie group to drive the quadrotor to its desired attitude. It is shown theoretically by Lyapunov techniques and LaSalle's invariance theorem that the equilibrium point of the overall system is asymptotically stable. As illustrated by experimental results, the proposed control law presents advantages such as high control precision, effective payload swing suppression, and so on.
Factors Associated with Prevalent Tuberculosis Among Patients Receiving Highly Active Antiretroviral Therapy in a Nigerian Tertiary Hospital

Background: Tuberculosis (TB) causes significant morbidity/mortality among human immunodeficiency virus-infected individuals in Africa. Reducing TB burden in the era of highly active antiretroviral therapy (HAART) is a public health priority. Aim: We determined the factors associated with prevalent TB among patients receiving HAART. Subjects and Methods: We conducted a cross-sectional study of adult patients who had received HAART for ≥12 weeks in a Nigerian tertiary hospital. Patients whose TB diagnosis predated HAART were excluded from the study. Pre-HAART data were collected from the clinic records, whereas post-HAART data were obtained through medical history, physical examination, and laboratory investigations. Standard TB screening/diagnostic algorithms as applicable in Nigeria were used. Logistic regression analysis was used to determine factors independently associated with prevalent TB. Results: about 65.8% (222/339) were women. The mean age was 41.1 (10.0) years and 23.6% (73/339) had past history of TB. The prevalence of active TB was 7.7% (26/339). Among these patients, 42.3% (11/26) had pulmonary TB, 34.6% (9/26) had disseminated TB, whereas 23.1% (6/26) had only extra-pulmonary disease. Only 45% (9/20) of patients with pulmonary involvement had positive sputum smear. Factors independently associated with prevalent TB were lower social class (adjusted odds ratio [aOR]: 31.7; 95% confidence interval [CI]: 1.1–1417.3), HAART non-adherence (aOR125.5; 95% CI: 9.6–1636.3), baseline CD4 <200cells/μl (aOR31.0; 95%CI: 1.6–590.6), previous TB (aOR13.8; 95% CI: 2.0–94.1), and current hemoglobin <10 g/dl (aOR10.3; 95% CI: 1.1–99.2). Conclusion: Factors associated with prevalent TB were a lower social class, HAART non-adherence, severe immunosuppression before HAART initiation, previous TB, and anemia post-HAART. TB case finding should be intensified in these high-risk groups.
Dayside auroral activity and magnetic flux transfer from the solar wind

Combined observations by meridian-scanning photometers and the EISCAT radar show that the "midday-auroral breakup" phenomenon is associated with major increases in ionospheric flow. A sequence of nine events is observed in the early afternoon MLT sector during a period when the IMF is strongly southward with a large positive By component. Each auroral structure is seen at both 630 and 557.7nm and initially moves westward, accompanied by an increase in potential of 30-60kV across the north-south dimension of the EISCAT field-of-view. After a few minutes the arc (or arc fragment) moves into the polar cap and fades, and the velocities observed by the radar swing from westward toward northward. We conclude that dayside auroral breakup is closely associated with momentum transfer across the magnetopause which occurs in a series of events 5-15 minutes apart. The largest of the observed events has dimensions of about 300km (in the direction of westward motion) by 700km, is bounded on its poleward edge by a 5kR arc and is associated with a potential of at least 80kV.