Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic studies associated with Parkinson’s disease

ABSTRACT Introduction: Parkinson’s disease (PD) is an insidious disorder affecting more than 1–2% of the population over the age of 65. Understanding the etiology of PD may create opportunities for developing new treatments. Genomic and transcriptomic studies are useful, but do not provide evidence for the actual status of the disease. Conversely, proteomic studies deal with proteins, which are real time players, and can hence provide information on the dynamic nature of the affected cells. The number of publications relating to the proteomics of PD is vast. Therefore, there is a need to evaluate the current proteomics literature and establish the connections between the past and the present to foresee the future. Areas covered: PubMed and Web of Science were used to retrieve the literature associated with PD proteomics. Studies using human samples, model organisms and cell lines were selected and reviewed to highlight their contributions to PD. Expert commentary: The proteomic studies associated with PD achieved only limited success in facilitating disease diagnosis, monitoring and progression. A global system biology approach using new models is needed. Future research should integrate the findings of proteomics with other omics data to facilitate both early diagnosis and the treatment of PD.
Quantitative and qualitative feed restriction on growth characteristics of male broiler chickens.

Four experiments were conducted to evaluate the quantitative and qualitative feed restriction on the performance of male broiler chickens. In the first experiment, broilers fed identical pelleted diets were feed-restricted from 5 to 42 d by giving 95, 90, or 85% of the feed consumed ad libitum by control birds the previous day. In a second experiment, broilers were fed pellet or mash diets from 1 to 7 wk. In Experiments 3 and 4, broilers were feed-restricted to 90% of the ad libitum intake of a control group during different intervals. Results from Experiment 1 indicated that live body weight at 42 d was significantly different between unrestricted and restricted broilers (P < 0.01). A reduction in mortality was noted when feed intake was reduced (P < 0.05). In the second experiment, broilers fed mash had lower body weights and breast meat yields at 42 and 49 d (P < 0.05). Cumulative mortality at 42 and 49 d was reduced in broilers fed mash (P < 0.05). Results from Experiment 3 indicated that body weight and mortality were not significantly different (P > 0.05) at 42 d across treatments. There was a significant (P < 0.01) linear improvement on feed conversion at 42 d due to duration of feed restriction. Breast meat yield at 42 d was less in broilers subjected to mild feed restriction (P > 0.05) (Experiments 3 and 4). Broilers appeared able to recover from mild feed restriction, and there was always an associated reduction in mortality.
Enhanced active‐feedback frequency compensation with on‐chip‐capacitor reduction feature for amplifiers with large capacitive load

A large capacitive load amplifier with enhanced active‐feedback frequency compensation is proposed in this paper. The enhancement is achieved through using a wide‐bandwidth scalar circuit to increase the transconductance of the output stage so that the overall bandwidth of the amplifier can be extended considerably. Implemented in a standard CMOS 130‐nm technology, with a supply of 0.7 V and consuming 27 μA of current, the amplifier drives a load capacitor of 15 nF. No on‐chip resistor is needed; only a 0.91‐pF compensation capacitor is used to maintain stability. The achieved gain‐bandwidth product and phase margin are 1.28 MHz and 66.9°, respectively. Moreover, the slew rate is 0.263 V/μs. The active chip area is 0.0056 mm2. Copyright © 2017 John Wiley & Sons, Ltd.
The effect of feeding programs on reproductive traits and selected blood chemistries of caged broiler breeder males.

The effects of five different feeding levels [136, 125, 113, 102, and 91 g/male/day of a 13.1% crude protein (CP), 3167 kcal metabolizable energy (ME)/kg feed] were evaluated on the reproductive traits of caged adult broiler breeder males from 30 to 60 weeks of age. Individual body weights, semen volume, sperm cells per ejaculate, and fertilizing ability were measured at 30, 40, 50, and 60 weeks of age. To assist in measuring the effect of feed restriction on metabolism during these periods, average hematocrits, plasma cholesterol, total protein, and uric acid levels were analyzed. Significant (P less than .05) reductions were observed in average body weights, semen volume, sperm cell numbers per ejaculate, testicular weights, and hematocrits with feed restriction at the 91-g compared to the 136-g feeding level. At 40 weeks of age, the percent of males producing semen was significantly reduced for the 102-and 91-g compared to the 136-g feeding level. Average plasma cholesterol levels were significantly increased at the 91-g compared to the 136-g feeding level, but little effect was observed in plasma total protein and uric acid levels. Correlation coefficients were negative for plasma cholesterol to body weights, sperm numbers per ejaculate, and testicular weights but positive for body weights to hematocrits and testicular weights.
Dynamic Matching: Reducing Integral Algorithms to Approximately-Maximal Fractional Algorithms

We present a simple randomized reduction from fully-dynamic integral matching algorithms to fully-dynamic approximately-maximal" fractional matching algorithms. Applying this reduction to the recent fractional matching algorithm of Bhattacharya, Henzinger, and Nanongkai (SODA 2017), we obtain a novel result for the integral problem. Specifically, our main result is a randomized fully-dynamic $(2+\epsilon)$-approximate integral matching algorithm with small polylog worst-case update time. For the $(2+\epsilon)$-approximation regime only a fractional fully-dynamic $(2+\epsilon)$-matching algorithm with worst-case polylog update time was previously known, due to Bhattacharya et al.~(SODA 2017). Our algorithm is the first algorithm that maintains approximate matchings with worst-case update time better than polynomial, for any constant approximation ratio.
Recognizing and Overcoming Difficult Site Conditions for Afforestation of Bottomland Hardwoods

SEPTEMBER 2004 183 In the last decade, about 370,000 acres (150,000 ha) of economically marginal farmland in the Lower Mississippi Alluvial Valley (LMAV) have been restored to bottomland hardwood forests (Stanturf and others 1998, King and Keeland 1999, Schoenholtz and others 2001). Planting of this considerable acreage is due to several federal programs, such as the Wetlands Reserve Program (WRP), that assist landowners by financing afforestation (Figure 1). Unfortunately, these operational plantings have not performed as well as smaller plantings or research plots (Stanturf and others 2001a). For example, a recent survey of WRP plantings in westcentral Mississippi revealed that more than 90 percent of the sites failed to meet the criteria of 100 woody stems per acre (247 stems per ha) three years after planting or direct seeding. While planting 1-0 bareroot seedlings of oak was more successful than direct-seeding acorns, only 23 percent of the land planted with seedlings met the criteria (C.J. Schweitzer unpublished data). Planting and direct seeding oak (Quercus spp.) on public land in the same area has been more successful. Meanwhile, Allen (1990) found 70 percent of the planted bottomland hardwood stands on the national wildlife refuges he evaluated had more than 200 trees per acre (494 stems per ha). We believe that the recurring problems in operational plantings on private lands are due in part to the failure of planters to recognize adverse site conditions and their failure to use appropriate methods for overcoming site limitations. Our objectives in this paper are to synthesize research and experience into guidelines for recognizing adverse site conditions due to hydroperiod, soil, competing vegetation, and herbivory. We describe techniques for overcoming these conditions and suggest promising research areas.
Ras to Extracellular Signal-Regulated Kinase Signaling Proteomic and Functional Genomic Landscape of Receptor Tyrosine

4 Science Signaling Berger and Norbert Perrimon (25 October 2011) Svetlana Pacifico, Thilakam Murali, Russell L. Finley, Jr., John M. Asara, Bonnie Porto, Vinayagam, Yanhui Hu, Richard Binari, Pengyu Hong, Xiaoyun Sun, Maura Adam A. Friedman, George Tucker, Rohit Singh, Dong Yan, Arunachalam Kinase and Ras to Extracellular Signal-Regulated Kinase Signaling Proteomic and Functional Genomic Landscape of Receptor Tyrosine `
Evaluation of dietary supplements of lipase, detergent, and crude porcine pancreas on fat utilization by young broiler chicks.

The purpose of Experiment 1 was to improve the digestibility of fat through the use of supplemental lipase enzymes. A 2 x 3 factorial arrangement of treatments involving two levels of animal-vegetable blend fat (AV) (4 and 8%) and three enzyme treatments, namely none; Pancreatic, 0.714%; and Pancreatin, 0.714%, were randomly allocated within a battery brooder. There was an increase in diet ME and apparent fat digestibility when Pancreatic and Pancreatin enzymes were used (P < 0.01). However, both enzymes caused lower feed intake and lower BW gain (P < 0.01). In Experiment 2, Pancreatic enzyme was used at graded levels of 0, 0.214, 0.429, 0.643, 0.857, and 1.071%, involving 4% dietary AV fat. The ME values were greater as the enzyme level increased (P < 0.01). However, as found in Experiment 1 lower feed intake and BW gain were observed with all enzyme levels compared with the control group. There was a linear effect on feed intake and BW gain (P < 0.01) and a quadratic effect on apparent fat digestibility (P < 0.05) and feed utilization (P < 0.01). Experiment 3 was designed to test the effect of Pancreatic enzyme at 0 or 1.339% in combination with two levels of detergent, namely 0 and 10% (with 4% added AV). The detergent used consisted of a mixture of 95% Span 60 and 5% Tween 60. In general, there was no significant effect of detergent (P > 0.05). Experiment 4 was conducted to test the effect of supplementation of graded levels of ground crude porcine pancreas at 0, 0.321, 0.535, 0.750, 0.964, 1.178, or 1.392% of the diet on performance of male broiler chicks to confirm the anorexic effect caused by supplementing with Pancreatic enzyme. In general, there was no significant effect of feeding crude porcine pancreas on the performance of male broiler chicks (P > 0.05). In these studies, lipase enzymes improved fat digestion, although it is suspected that associated reduced feed intake may be associated with contaminants such as cholecystokinin hormone.
MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation

Motivation: The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels. Results: We present a method to jointly model read counts from bisulfite sequencing, oxidative bisulfite sequencing and Tet-Assisted Bisulfite sequencing, providing simultaneous estimates of 5-hmC and 5-mC levels that are consistent across experiment types. Availability: http://smithlab.usc.edu/software/mlml Contact: andrewds@usc.edu Supplementary information: Supplementary material is available at Bioinformatics online.
Improvement of mechanical properties by incorporating graphene oxide into cement mortar

ABSTRACT As a two-dimensional nanomaterial, graphene oxide has attracted much attention for its use in reinforcing cementitious materials. However, the dispersion of graphene oxide in cementitious materials has been found unsatisfactory due to crosslinking of divalent calcium ions. In this study, we propose a modified mixing procedure to improve graphene oxide dispersion in cement mortar by utilizing silica sand to mechanically separate graphene oxide nanosheets. Apart from the improved graphene oxide dispersion, adhesion between sand and cement matrix is also believed to be enhanced due to the improved roughness of the sand surface. According to our mechanical properties study, with the introduction of 0.02% by weight graphene oxide in cement mortar, compressive strength was significantly improved by more than 25% and tensile splitting and flexural strength were improved by around 15%. In a microstructural investigation, the interfacial transition zone in cement mortar was found to be denser due to the addition of graphene oxide. Moreover, graphene oxide incorporated cement mortar also showed pore structure refinement and porosity reduction. Therefore, improvement in mechanical properties may result from an improved interfacial transition zone and a more refined pore structure with the introduction of a small quantity of well-dispersed graphene oxide nanosheets.
Flow Induced Crystallization of Poly(ether‐block‐amide) from the Microinjection Molding Process and its Effect on Mechanical Properties

Crystallization during microinjection molding is investigated relative to process conditions. Modulus and hardness of the skin layer are higher than the core layer, regardless of core structure. Young's modulus, strain at break and yield stress all increase with an increase of skin ratio. The relationship between process, morphology and mechanical properties is studied for micro products. By using in-line process monitoring, flow induced crystallization is characterized by shear stress and apparent specific work. Shear stress is shown to be a good candidate to characterize the formation of highly oriented structures under actual microinjection molding processes. This may provide a method for in-line control of morphology development, and then final properties, by controlling the flow conditions.
Development of lipase activity in yolk membrane and pancreas of young turkeys.

Two experiments were conducted to determine the development of lipase activity in the yolk membrane (YM) of poults during the embryonic period and in the pancreas during the first 16 days after hatching. A corn-soybean meal diet, formulated to contain 6% supplemental fat was used in both Experiments 1 and 2; two dietary levels (0 or .06%) of sodium taurodeoxycholate (NaTDC) were tested in Experiment 2. Samples of YM and pancreas were collected starting at Day 7 (Experiment 1) and at Day 18 (Experiment 2) of incubation and continued until Day 4 and Day 16 after hatching for YM and pancreas, respectively. Lipase activity was measured titrametrically and tributyrin was used as the reaction substrate. Total lipase activity (TLA) per YM increased from 31 mueq/min at Day 9 of incubation to a maximum of 214 mueq/min at Day 21 and then decreased through Day 4 after hatching. Specific lipase activity as lipase activity per milligram of pancreas dry weight (DW) increased from 3.1 mueq/mgDW/min at Day 27 of incubation to 15.6 mueq/mgDW/min at Day 1 after hatching. This increase continued linearly (P less than .001) to 26.2 mueq/mgDW/min by Day 16 after hatching. The TLA per pancreas averaged 400 mueq/min at Day 1 and increased to 13,000 (Experiment 1) and 8,400 (Experiment 2) mueq/min by Day 16 after hatching. Inclusion of NaTDC in the diet had no effect on pancreatic lipase activity.
Engraftment, neuroglial transdifferentiation and behavioral recovery after complete spinal cord transection in rats

Background: Proof of the efficacy and safety of a xenogeneic mesenchymal stem cell (MSCs) transplant for spinal cord injury (SCI) may theoretically widen the spectrum of possible grafts for neuroregeneration. Methods: Twenty rats were submitted to complete spinal cord transection. Ovine bone marrow MSCs, retrovirally transfected with red fluorescent protein and not previously induced for neuroglial differentiation, were applied in 10 study rats (MSCG). Fibrin glue was injected in 10 control rats (FGG). All rats were evaluated on a weekly basis and scored using the Basso–Beattie–Bresnahan (BBB) locomotor scale for 10 weeks, when the collected data were statistically analyzed. The spinal cords were then harvested and analyzed with light microscopy, immunohistochemistry, and immunofluorescence. Results: Ovine MSCs culture showed positivity for Nestin. MSCG had a significant and durable recovery of motor functions (P <.001). Red fluorescence was found at the injury sites in MSCG. Positivity for Nestin, tubulin βIII, NG2 glia, neuron-specific enolase, vimentin, and 200 kD neurofilament were also found at the same sites. Conclusions: Xenogeneic ovine bone marrow MSCs proved capable of engrafting into the injured rat spinal cord. Transdifferentiation into a neuroglial phenotype was able to support partial functional recovery.
Strategic Influence in Social Networks

We consider a model of influence with a set of non-strategic agents and two strategic agents. The non-strategic agents have initial opinions and are linked through a simply connected network. They update their opinions as in the DeGroot model. The two strategic agents have fixed opinions, 1 and 0 respectively, and are characterized by the magnitude of the impact they can exert on non-strategic agents. Each strategic agent forms a link with one non-strategic agent in order to alter the average opinion that eventually emerges in the network. This procedure defines a zero-sum game whose players are the two strategic agents and whose strategy set is the set of non-strategic agents. We focus on the existence and the characterization of equilibria in pure strategy in this setting. Simple examples show that the existence of a pure strategy equilibrium does depend on the structure of the network. The characterization of equilibrium we obtain emphasizes on the one hand the influenceability of target agents and on the other hand their centrality whose natural measure in our context defines a new concept, related to betweenness centrality, that we call intermediacy. We also show that in the case where the two strategic agents have the same impact, symmetric equilibria emerge as natural solutions whereas in the case where the impacts are uneven, the strategic players generally have differentiated equilibrium targets, the high-impacts agent focusing on centrality and the low-impact agent on influenceability.
Deterministic Regular Expressions with Back-References

Most modern libraries for regular expression matching allow back-references (i.e., repetition operators) that substantially increase expressive power, but also lead to intractability. In order to find a better balance between expressiveness and tractability, we combine these with the notion of determinism for regular expressions used in XML DTDs and XML Schema. This includes the definition of a suitable automaton model, and a generalization of the Glushkov construction. We demonstrate that, compared to their non-deterministic superclass, these deterministic regular expressions with back-references have desirable algorithmic properties (i.e., efficiently solvable membership problem and some decidable problems in static analysis), while, at the same time, their expressive power exceeds that of deterministic regular expressions without back-references.
Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction

Median lethal death, LD50, is a general indicator of compound acute oral toxicity (AOT). Various in silico methods were developed for AOT prediction to reduce costs and time. In this study, we developed an improved molecular graph encoding convolutional neural networks (MGE-CNN) architecture to construct three types of high-quality AOT models: regression model (deepAOT-R), multiclassification model (deepAOT-C), and multitask model (deepAOT-CR). These predictive models highly outperformed previously reported models. For the two external data sets containing 1673 (test set I) and 375 (test set II) compounds, the R2 and mean absolute errors (MAEs) of deepAOT-R on the test set I were 0.864 and 0.195, and the prediction accuracies of deepAOT-C were 95.5% and 96.3% on test sets I and II, respectively. The two external prediction accuracies of deepAOT-CR are 95.0% and 94.1%, while the R2 and MAE are 0.861 and 0.204 for test set I, respectively. We then performed forward and backward exploration of deepAOT models for deep fingerprints, which could support shallow machine learning methods more efficiently than traditional fingerprints or descriptors. We further performed automatic feature learning, a key essence of deep learning, to map the corresponding activation values into fragment space and derive AOT-related chemical substructures by reverse mining of the features. Our deep learning architecture for AOT is generally applicable in predicting and exploring other toxicity or property end points of chemical compounds. The two deepAOT models are freely available at http://repharma.pku. edu.cn/DLAOT/DLAOThome.php or http://www.pkumdl. cn/DLAOT/DLAOThome.php .
Serum Vaspin Concentration in Elderly Type 2 Diabetes Mellitus Patients with Differing Body Mass Index: A Cross-Sectional Study

Aims. This study was to evaluate the association of serum vaspin concentrations with body mass index (BMI) among elderly patients (>60 years old). Methods. A total of 227 elderly individuals included 76 healthy with normal glucose tolerance, which divided into normal weight control (BMI < 25, n = 38) and overweight or obese control (BMI ≥ 25, n = 38) subgroups, and 150 T2DM patients, which divided into normal weight diabetes (BMI < 25, n = 55), overweight diabetes (30 > BMI ≥ 25, n = 52), and obese diabetes (BMI ≥ 30, n = 43) subgroups. Relevant parameters were matched for age and gender ratio. Serum vaspin concentrations were measured by enzyme-linked immunosorbent assay. Results. Serum vaspin concentration was significantly higher in the T2DM than the healthy (451.9 ± 32.6 versus 284.2 ± 21.7, P < 0.01). In the diabetic patients, the vaspin concentration was significantly higher in the obese group than the normal weight group (498.2 ± 17.1 versus 382.1 ± 21.3, P < 0.05). In addition, the concentration of vaspin in normal weight T2DM was higher than in healthy control group with normal weight (382.1 ± 21.3 versus 192.5 ± 45.2, P < 0.05). Multiple regression analysis revealed that BMI was independent factors influencing the serum vaspin concentration in all participants. Conclusion. Vaspin may play an important compensatory role in obesity and insulin resistance in elderly people. The clinical trial registration number is ChiCTR-OPC-14005698.
Point‐of‐Care Identification of Bacteria Using Protein‐Encapsulated Gold Nanoclusters

The rapid, simple, and reliable identification of the most prevalent pathogens is essential for clinical diagnostics, biology, and food safety. Herein, four protein‐encapsulated gold nanoclusters (protein–AuNCs) are designed and prepared as a sensor array for rapid identification of bacteria. The discrimination of six kinds of bacteria, including two kinds of drug‐resistant bacteria, is successfully realized by the as‐fabricated sensor array. The strategy presented here shows the advantages of easy synthesis and convenient to use. Furthermore, 100% classification accuracy is achieved by the sensor array consisting of two protein–AuNCs probes, demonstrating the design with sufficient diagnostic capacity. Taken together, the developed sensor array holds great promise for facile diagnosis of bacterial infection in resource‐limited settings.