Miracle-dz/UniFAR-FTUs huggingface dataset:
Training Generative Adversarial Networks via Primal-Dual Subgradient Methods: A Lagrangian Perspective on GAN

We relate the minimax game of generative adversarial networks (GANs) to finding the saddle points of the Lagrangian function for a convex optimization problem, where the discriminator outputs and the distribution of generator outputs play the roles of primal variables and dual variables, respectively. This formulation shows the connection between the standard GAN training process and the primal-dual subgradient methods for convex optimization. The inherent connection does not only provide a theoretical convergence proof for training GANs in the function space, but also inspires a novel objective function for training. The modified objective function forces the distribution of generator outputs to be updated along the direction according to the primal-dual subgradient methods. A toy example shows that the proposed method is able to resolve mode collapse, which in this case cannot be avoided by the standard GAN or Wasserstein GAN. Experiments on both Gaussian mixture synthetic data and real-world image datasets demonstrate the performance of the proposed method on generating diverse samples.
Morphological Development of Hydrating Tricalcium Silicate as Examined by Electron Microscopy Techniques

This study of C3S hydrates used a high-voltage electron microscope equipped with a gas reaction cell that allows the specimen to be kept moist, and high-resolution scanning and scanning transmission microscopes. Mechanical thinning and ion-beam thinning coupled with fractography allowed this study of microstructural development with time, enabling both the morphologies and the spatial relations of the morphologies to be observed. The combination of several microscopic techniques allowed the hydration products of C3S to be classified and compared with those of Diamond for portland cement hydrates.
On the Palette Index of Complete Bipartite Graphs

Abstract The palette of a vertex x of a graph G determined by a proper edge colouring φ of G is the set {φ(xy) : xy ∈ E(G)} and the diversity of φ is the number of different palettes determined by φ. The palette index of G is the minimum of diversities of φ taken over all proper edge colourings φ of G. In the article we determine the palette index of Km,n for m ≤ 5 and pose two conjectures concerning the palette index of complete bipartite graphs.
Incremental and decremental training for linear classification

In classification, if a small number of instances is added or removed, incremental and decremental techniques can be applied to quickly update the model. However, the design of incremental and decremental algorithms involves many considerations. In this paper, we focus on linear classifiers including logistic regression and linear SVM because of their simplicity over kernel or other methods. By applying a warm start strategy, we investigate issues such as using primal or dual formulation, choosing optimization methods, and creating practical implementations. Through theoretical analysis and practical experiments, we conclude that a warm start setting on a high-order optimization method for primal formulations is more suitable than others for incremental and decremental learning of linear classification.
Discrimination and Telomere Length Among Older Adults in the United States

Objectives: Chronic stress from experiencing discrimination can lead to long-term changes in psychological and physiologic responses, including shorter leukocyte telomere length. We examined the association between leukocyte telomere length and variations in the association by race or type of discrimination. Methods: Our study consisted of 3868 US-born non-Hispanic black (hereinafter, black) and non-Hispanic white (hereinafter, white) adult participants from the 2008 Health and Retirement Study biomarker sample with complete sociodemographic and discrimination information. We examined major lifetime unfair treatment and everyday discrimination. Coarsened exact matching matched exposed and unexposed participants on several sociodemographic factors. Coarsened exact matching creates analytic weights for the matched data sets. We applied weighted linear regression to the matched data sets. We conducted 2 subanalyses in which we matched on potential mediators—physical activity, smoking status, and obesity—and examined if racism was associated with shorter telomere length compared with other attributes. All analyses were stratified by race. Results: We found no difference in telomere length for black and white participants reporting major lifetime unfair treatment (β = 0.09; 95% CI, –0.33 to 0.15) or everyday discrimination (β = 0.04; 95% CI, –0.12 to 0.40). Everyday discrimination was associated with shorter leukocyte telomere length among black people (β = –0.23; 95% CI, –0.44 to –0.01) but not among white people (β = 0.05; 95% CI, –0.01 to 0.10). Matching on potential mediators generally decreased the effect estimate among black people. Conclusions: Experiencing everyday discrimination was associated with shortened telomere length among older black adults. Further research is needed to understand the adverse physiologic effects of discrimination to create effective interventions.
Ferrisia gilli (Hemiptera: Pseudococcidae) Transmits Grapevine Leafroll-Associated Viruses

Abstract Several mealybug species are vectors of grapevine leafroll-associated viruses (GLRaV), which cause the economically important grapevine leafroll disease in grape-producing regions worldwide. The mealybug Ferrisia gilli Gullan is a new pest of grapevines in El Dorado County, located in the Sierra Foothill wine-growing region of California. GLRaV species 1, 2, 3, and 4LV have been detected in vineyards with symptomatic vines in the Sierra Foothills. We conducted controlled virus acquisition and transmission experiments using source vine accessions infected with different combinations of GLRaV. We determined that F. gilli acquired GLRaV 1, 2, 3, and 4LV, and transmitted GLRaV-3 and GLRaV-4LV to uninfected recipient vines. Like numerous other mealybug species, in addition to causing direct damage to vines, F. gilli poses a threat to the grape industry as a vector of economically damaging viruses.
Deep Predictive Coding Network for Object Recognition

Inspired by predictive coding in neuroscience, we designed a bi-directional and recurrent neural net, namely deep predictive coding networks (PCN). It uses convolutional layers in both feedforward and feedback networks, and recurrent connections within each layer. Feedback connections from a higher layer carry the prediction of its lower-layer representation; feedforward connections carry the prediction errors to its higher-layer. Given image input, PCN runs recursive cycles of bottom-up and top-down computation to update its internal representations to reduce the difference between bottom-up input and top-down prediction at every layer. After multiple cycles of recursive updating, the representation is used for image classification. In training, the classification error backpropagates across layers and in time. With benchmark data (CIFAR-10/100, SVHN, and MNIST), PCN was found to always outperform its feedforward-only counterpart: a model without any mechanism for recurrent dynamics, and its performance tended to improve given more cycles of computation over time. In short, PCN reuses a single architecture to recursively run bottom-up and top-down process, enabling an increasingly longer cascade of non-linear transformation. For image classification, PCN refines its representation over time towards more accurate and definitive recognition.
Timing Determination of Invasive Fungal Infection Prophylaxis According to Immune Function in HSCT Patients

Patients who receive a hematopoietic stem cell transplantation (HSCT) exhibit an immune defect after recovering from neutropenia. The current guidelines do not recommend fungal prophylaxis in these patients, except for grades III to IV GVHD in HSCT. Thus, the timing for the initiation and cessation of IFI prophylaxis in immune-compromised patients remains a challenging endeavor. We retrospectively analyzed patients who received auto or allo-HSCT and monitored their immune function after recovering from neutropenia by measuring the levels of IgG, IgA, IgM, as well as the number of T, B, NK cells. We found that the level of IgG and NK cell count exhibited a significant difference with the incidence of IFI by logistic regression (p = 0.000 vs. 0.000, respectively) and conditional logistic regression (p = 0.009 vs. p = 0.002). The initiation of IFI prophylaxis was determined to be IgG < 7 mg/mL and NK cell count < 6.5 × 104/mL by an receiver operating characteristic curve separately. Tests in parallel increased the test sensitivity and specificity. Thus, the optimal timing for initiating prophylaxis in patients after HSCT could be IgG < 7 mg/mL or NK cell count < 6.5 × 104/mL. Future large-scale prospective clinical trials are required to verify these findings. Patients who are immuno-compromised after auto or allo-HSCT may benefit from a lower fungi infection incidence with immune surveillance and proper fungal prophylaxis.
Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre‐weaning

ABSTRACT This study aimed to characterize mucosa‐ and digesta‐associated microbiota in the hindgut (cecum, colon and rectum) of newborn (NB, n = 6), day 7 (n = 6), day 21 (n = 6) and day 42 (n = 6) Holstein bull calves using amplicon sequencing. The hindgut microbiota was diverse at birth, and mucosa‐attached microbial community had higher individual variation than that of digesta‐associated community. In total, 16 phyla were identified with Firmicutes, Bacteroidetes and Proteobacteria being the dominant microbial taxa in the hindgut. Quantitative real‐time PCR analysis showed a significant age effect on the proportion of mucosa‐attached Escherichia coli, Bifidobacterium, Clostridium cluster XIVa and Faecalibacterium prausnitzii. Especially, high abundance of mucosa‐associated Escherichia was detected during the first week of life, suggesting higher chance of the pathogenic infection during this stage. The relative abundances of predicted microbial genes involved in amino acid metabolism, carbohydrate metabolism and energy metabolism were enriched, indicating the importance of hindgut microbiota in fermentation during the pre‐weaned period. Moreover, the significant correlation between short‐chain fatty acid concentration and mucosa‐attached carbohydrate utilizing (Coprococcus 1, Blautia, Lachnospiraceae NC2004 group, etc.) and health‐related bacteria (Escherichia‐Shigella and Salmonella) suggests the importance of hindgut microbiota in the fermentation and health of dairy calves during pre‐weaned period.
Effect of lighting program and nutrition on reproductive performance of molted single comb White Leghorn hens.

Two adjoining rooms in a light-tight, fan-ventilated, insulated house were used for a study involving 320 Single Comb White Leghorn hens, 60 wk of age, placed two per cage. These hens were subjected to an induced molt which compared two lighting programs, two molt rations, two levels of total sulfur amino acids (TSAA), and two levels of ascorbic acid (AA) in a factorial arrangement. There were four treatments. Treatment 1 compared the Washington lighting program (WSU), consisting of an 8-h light photoperiod for 28 days beginning 7 days before fast with the North Carolina program (NCSU), consisting of a 24-h light photoperiod for 7 days prior to fast followed by 12 h light/day for 21 days. After 28 days, light duration was increased to 16 h/day in stages for both programs. Treatment 2 consisted of feeding cracked corn (CC) or 16% protein molt ration (MR) for 2 weeks: Treatment 3, feeding of 14% layer mash with either . 60% or . 65% TSAA; and Treatment 4, addition of either 0 or 50 ppm AA to the 14% layer mash. After molting, egg production was increased in the NCSU lighting program and . 65% TSAA treatments. Feed conversion was improved by the NCSU lighting treatment. Deaths were fewer in diets with 50 ppm AA. Egg weight, specific gravity, and shell weight were not affected by any treatment. A significant light X molt diet interaction occurred due to better performance of MR birds compared with CC birds in the NCSU lighting program, whereas on the WSU lighting program, CC produced better performance. These data indicated that combining features of various molt programs may not produce optimum results.
Evolution-Based Functional Decomposition of Proteins

The essential biological properties of proteins - folding, biochemical activities, and the capacity to adapt - arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function, but requires broad further testing by the scientific community. To facilitate this, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package. We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment - a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for understanding the structural basis for protein function and for generally testing the concept of sectors as the principal functional units of proteins.
High dietary zinc and fasting as methods of forced resting: a performance comparison.

A study was conducted to compare fasting and high dietary zinc as procedures to induce a forced rest of laying hens. Five to six replicates (25 hens each) of Single Comb White Leghorn hens laying approximately 60% were fasted for 10 days (fasted) or fed either 10,000 ppm zinc (10 Zn) or 20,000 ppm zinc (20 Zn) for a period of 4 days. A fourth treatment consisted of feeding 20,000 ppm zinc for 8 days (20 Zn-8). During the rest-inducing period, hens consumed little of either high zinc diet. Four-day intake by 20 Zn hens averaged 17.6 +/- . 2 g/hen/day compared to 32.6 +/- 1.5 g/hen/day (means +/- SEM) for 10 Zn hens. Those fed 20 Zn-8 consumed the least amount, 12.6 +/- . 2 g/hen/day during the 8 days of high zinc feeding. Body weight loss of hens in this last group was comparable to hens fasted for 10 days (fasted), i.e., 24.6 +/- . 3% vs. 27.6 +/- . 4%. Weight loss of hens in the remaining two groups reflected, to some extent, differences in feed consumption. The 20 Zn hens lost significantly more body weight during the 4-day period when compared with 10 Zn hens (16.2 +/- .4% vs. 11.9 +/- .5%). Each treatment resulted in a sharp drop in egg production. By the 5th day, fasted, 20 Zn, and 20 Zn-8 hens had ceased producing eggs. Egg production by 10 Zn hens declined at a slightly slower rate. There were considerable differences in post-rest egg production among the various treatments. (ABSTRACT TRUNCATED AT 250 WORDS)
The effect of testosterone propionate on growth of broiler chickens.

The effects of testosterone propionate (TP) on body weight, tissue percentages of body weight, serum IgM, and rectal temperature (2 h postinjection) of male and female broiler chickens were investigated at 28 and 48 days posthatching. Testosterone propionate was dissolved in sesame oil and was injected at 2 mg/kg of body weight every other day, and controls were treated with sesame oil at similar volume, starting Day 7 posthatching. Administration of TP reduced (P < .05) body weight and percentages of liver, testes, and bursa of Fabricius at 28 and 48 days of age. At 28 and 48 days of age, muscle percentage and comb growth of TP-treated birds increased (P < .05) but ovarian weight was unaffected. Concentrations of IgM in serum of TP-injected birds was unchanged at Day 28, but increased (P < .05) at Day 48. Testosterone propionate did not affect percentages of bone or abdominal fat in either sex. Rectal temperature was depressed (P < .05) by TP treatment in both sexes at both ages.
Suppressor of Overexpression of CO 1 Negatively Regulates Dark-Induced Leaf Degreening and Senescence by Directly Repressing Pheophytinase and Other Senescence-Associated Genes in Arabidopsis1

SOC1 inhibits dark-induced leaf degreening and senescence by directly binding to the CArG box of PPH, NYE1, and SAG113 promoters and inhibiting their expression at the transcriptional level in Arabidopsis. Although the biochemical pathway of chlorophyll (Chl) degradation has been largely elucidated, how Chl is rapidly yet coordinately degraded during leaf senescence remains elusive. Pheophytinase (PPH) is the enzyme for catalyzing the removal of the phytol group from pheophytin a, and PPH expression is significantly induced during leaf senescence. To elucidate the transcriptional regulation of PPH, we used a yeast (Saccharomyces cerevisiae) one-hybrid system to screen for its trans-regulators. SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), a key flowering pathway integrator, was initially identified as one of the putative trans-regulators of PPH. After dark treatment, leaves of an SOC1 knockdown mutant (soc1-6) showed an accelerated yellowing phenotype, whereas those of SOC1-overexpressing lines exhibited a partial stay-green phenotype. SOC1 and PPH expression showed a negative correlation during leaf senescence. Substantially, SOC1 protein could bind specifically to the CArG box of the PPH promoter in vitro and in vivo, and overexpression of SOC1 significantly inhibited the transcriptional activity of the PPH promoter in Arabidopsis (Arabidopsis thaliana) protoplasts. Importantly, soc1-6 pph-1 (a PPH knockout mutant) double mutant displayed a stay-green phenotype similar to that of pph-1 during dark treatment. These results demonstrated that SOC1 inhibits Chl degradation via negatively regulating PPH expression. In addition, measurement of the Chl content and the maximum photochemical efficiency of photosystem II of soc1-6 and SOC1-OE leaves after dark treatment suggested that SOC1 also negatively regulates the general senescence process. Seven SENESCENCE-ASSOCIATED GENES (SAGs) were thereafter identified as its potential target genes, and NONYELLOWING1 and SAG113 were experimentally confirmed. Together, we reveal that SOC1 represses dark-induced leaf Chl degradation and senescence in general in Arabidopsis.
Effect of lactic acid administration in the drinking water during preslaughter feed withdrawal on Salmonella and Campylobacter contamination of broilers.

The crop is a known source of Salmonella and Campylobacter contamination. We evaluated the use of selected organic acids (0.5% acetic, lactic, or formic) in drinking water during a simulated 8-h pretransport feed withdrawal (FW). Salmonella typhimurium was recovered from 53/100 control crops and from 45/100 of crops from acetic acid-treated broilers. However, treatment with lactic acid (31/100) or formic acid (28/76) caused significant (P < 0.05) reduction in incidence. Reductions of recovered incidence were also associated with reduced numbers of S. typhimurium recovered (e.g., control, log 1.45 cfu/crop; lactic acid, 0.79 cfu/crop). In an additional commercial farm study, broilers were provided 0.44% lactic acid during a 10-h FW (4 h on the farm and 6 h transport) and pre-FW crop, post-FW crop, and pre-chill carcass wash samples were collected for Campylobacter and Salmonella detection. Crop contamination with Salmonella was significantly reduced by lactic acid treatment (6/175) as compared with controls (29/175). Importantly, Salmonella isolation incidence in prechill carcass rinses was significantly reduced by 52.4% with the use of lactic acid (26/175 vs. 55/176). Crop contamination with Campylobacter was significantly reduced by lactic acid treatment (62.3%) as compared with the controls (85.1%). Lactic acid also reduced the incidence of Campylobacter found on pre-chill carcass rinses by 14.7% compared with the controls. These studies suggest that incorporation of lactic acid in the drinking water during pretransport FW may reduce Salmonella and Campylobacter contamination of crops and broiler carcasses at processing.
RNA-Seq investigation and in vivo study the effect of strontium ranelate on ovariectomized rat via the involvement of ROCK1

Abstract Strontium ranelate (SrR) is an anti-osteoporosis drug with excellent osteogenic and angiogenic capacity. In this study, we aimed to investigate the osteogenesis and angiogenesis effects of SrR and the underlying mechanism involved. RNA-Seq was conducted to examine the effects of SrR on gene expression in ovariectomy rat bone marrow mesenchymal stem cells (OVX-rBMSCs). To validate the different expressed gene in vitro, the effects of gene interference and overexpression in osteogenic induction environment of OVX-rBMSCs and in primary osteoblasts were studied. RNA-Seq showed that ROCK1 significantly increased after SrR treatment in OVX-rBMSCs, and further validated by real-time PCR and western blotting. Overexpression of ROCK1 promoted osteogenic differentiation of OVX-rBMSCs and induced cell viability and inhibited apoptosis of primary osteoblasts, which was reversed by inhibition of ROCK1 by RNA interference or ROCK1 inhibitor (Y-27632) after SrR treatment. Furthermore, the SrR was loaded on nano-structured hydroxyapatite (nano-HAp) particulates to promote osteogenesis and angiogenesis in repairing of the femoral condyle bone defect using ovariectomy rat model. Taken together, ROCK1 is one of the targets that SrR promotes the osteogenic differentiation of OVX-rBMSCs and cell viability of primary osteoblasts, the nano-HAp particles could act as carriers for SrR to repair bone defects.
Copper Oxide Nanoparticles Induced Mitochondria Mediated Apoptosis in Human Hepatocarcinoma Cells

Copper oxide nanoparticles (CuO NPs) are heavily utilized in semiconductor devices, gas sensor, batteries, solar energy converter, microelectronics and heat transfer fluids. It has been reported that liver is one of the target organs for nanoparticles after they gain entry into the body through any of the possible routes. Recent studies have shown cytotoxic response of CuO NPs in liver cells. However, the underlying mechanism of apoptosis in liver cells due to CuO NPs exposure is largely lacking. We explored the possible mechanisms of apoptosis induced by CuO NPs in human hepatocellular carcinoma HepG2 cells. Prepared CuO NPs were spherical in shape with a smooth surface and had an average diameter of 22 nm. CuO NPs (concentration range 2–50 µg/ml) were found to induce cytotoxicity in HepG2 cells in dose-dependent manner, which was likely to be mediated through reactive oxygen species generation and oxidative stress. Tumor suppressor gene p53 and apoptotic gene caspase-3 were up-regulated due to CuO NPs exposure. Decrease in mitochondrial membrane potential with a concomitant increase in the gene expression of bax/bcl2 ratio suggested that mitochondria mediated pathway involved in CuO NPs induced apoptosis. This study has provided valuable insights into the possible mechanism of apoptosis caused by CuO NPs at in vitro level. Underlying mechanism(s) of apoptosis due to CuO NPs exposure should be further invested at in vivo level.