Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacillus subtilis and yeast cell wall improve the intestinal health of broilers challenged by Clostridium perfringens

ABSTRACT 1. The objective was to investigate the effects of Bacillus subtilis, yeast cell wall (YCW) and their combination on intestinal health of broilers challenged by Clostridium perfringens over a 21-d period. 2. Using a 5 × 2 factorial arrangement of treatments, 800 1-d-old male Cobb 500 broilers were used to study the effects of feed additives (without additive or with zinc bacitracin, B. subtilis, YCW, and the combination of B. subtilis and YCW), pathogen challenge (without or with Clostridium perfringens challenge), and their interactive effects. 3. C. perfringens infection increased intestinal lesions scores, damaged intestinal histomorphology, increased serum endotoxin concentration, cytokine mRNA expression and intestinal population of C. perfringens and Escherichia coli and decreased ileal bifidobacteria numbers. The 4 additives decreased serum endotoxin. Zinc bacitracin tended to decrease cytokine mRNA expression and the intestinal number of C. perfringens and E. coli. B. subtilis, YCW and their combination increased cytokine mRNA expression. B. subtilis and YCW decreased the number of C. perfringens and E. coli in the ileum, and their combination decreased pathogens numbers in the ileum and caecum. 4. In conclusion, B. subtilis, YCW and their combination improved the intestinal health of NE-infected broilers, and could be potential alternatives to antibiotics.
Prevention of inflammation-mediated bone loss in murine and canine periodontal disease via recruitment of regulatory lymphocytes

Significance Periodontal disease (gum disease) is an extremely prevalent inflammatory disease initiated by persistent bacterial insult, leading to the destruction of bone and gingival tissues. Current clinical treatments focus solely on the removal of bacteria. In this study, we put forth a strategy to address the underlying inflammatory imbalance in periodontal disease by harnessing the body’s own sophisticated immunoregulatory mechanisms through the recruitment of regulatory T cells (Tregs). This is accomplished by controllably releasing small quantities (nanogram/kilogram range) of chemokine recognized by Tregs using biodegradable, resorbable polymers with an excellent track record of regulatory approval. Administration of Treg-recruiting treatments to the gingiva of mice and canines reduces clinical scores of disease as well as hard and soft tissue destruction. The hallmark of periodontal disease is the progressive destruction of gingival soft tissue and alveolar bone, which is initiated by inflammation in response to an invasive and persistent bacterial insult. In recent years, it has become apparent that this tissue destruction is associated with a decrease in local regulatory processes, including a decrease of forkhead box P3-expressing regulatory lymphocytes. Accordingly, we developed a controlled release system capable of generating a steady release of a known chemoattractant for regulatory lymphocytes, C-C motif chemokine ligand 22 (CCL22), composed of a degradable polymer with a proven track record of clinical translation, poly(lactic-co-glycolic) acid. We have previously shown that this sustained presentation of CCL22 from a point source effectively recruits regulatory T cells (Tregs) to the site of injection. Following administration of the Treg-recruiting formulation to the gingivae in murine experimental periodontitis, we observed increases in hallmark Treg-associated anti-inflammatory molecules, a decrease of proinflammatory cytokines, and a marked reduction in alveolar bone resorption. Furthermore, application of the Treg-recruiting formulation (fabricated with human CCL22) in ligature-induced periodontitis in beagle dogs leads to reduced clinical measures of inflammation and less alveolar bone loss under severe inflammatory conditions in the presence of a diverse periodontopathogen milieu.
Effect of Body Thickness on the Electrical Performance of Ballistic n-Channel GaSb Double-Gate Ultrathin-Body Transistor

We investigated the effect of body thickness on the electrical performance of GaSb double-gate ultrathin-body (DG-UTB) MOSFET by examining the band structure of the 12- (~2 nm), 24- (~4 nm), 36- (~6 nm), and 48- (~8 nm) atomic-layer (AL) thick GaSb. Two different surface orientations, namely, (100) and (111), were studied. sp3d5s* tight-binding model is used to calculate the band structures of GaSb MOSFET. Ballistic transport was studied using the semiclassical top-of-barrier model with applied self-consistent real-space potential across the body. First, we found that for (100) surface orientation, GaSb DG-UTB FET with body thickness of 24 ALs offered relatively larger ON-state current for various gate dielectric materials studied. However, for (111) surface orientation, 12 ALs GaSb DG-UTB FET showed the best performance due to its reasonably higher injection velocity and larger electron density. Furthermore, for the FET with a body thickness of 48 ALs and HfO2 dielectric, it was observed that the charge occupations shift toward the surface, unlike the cases of FETs with thinner body, leading to the formation of inversion charge on the surface. Finally, we compared the ON-state current of GaSb DG-UTB FET with different channel surface orientations and found that (100) surface generally outperforms (111) surface in terms of ON-state current.
Linear Estimation of Treatment Effects in Demand Response: An Experimental Design Approach

Demand response aims to stimulate electricity consumers to modify their loads at critical time periods. In this paper, we consider signals in demand response programs as a binary treatment to the customers and estimate the average treatment effect, which is the average change in consumption under the demand response signals. More specifically, we propose to estimate this effect by linear regression models and derive several estimators based on the different models. From both synthetic and real data, we show that including more information about the customers does not always improve estimation accuracy: the interaction between the side information and the demand response signal must be carefully modeled. In addition, we compare the traditional linear regression model with the modified covariate method which models the interaction between treatment effect and covariates. We analyze the variances of these estimators and discuss different cases where each respective estimator works the best. The purpose of these comparisons is not to claim the superiority of the different methods, rather we aim to provide practical guidance on the most suitable estimator to use under different settings. Our results are validated using data collected by Pecan Street and EnergyPlus.
Visual judgments of length in the economics laboratory: Are there brains in stochastic choice?

We design a choice experiment where the objects are valued according to only a single attribute with a continuous measure and we can observe the true preferences of subjects. However, subjects have an imperfect perception of their own preferences. Subjects are given a choice set involving several lines of various lengths and are told to select one of them. They strive to select the longest line because they are paid an amount that is increasing in the length of their selection. Subjects also make their choices while they are required to remember either a 6-digit number (high cognitive load) or a 1-digit number (low cognitive load). We find that subjects in the high load treatment make inferior line selections and perform worse searches. When we restrict attention to the set of viewed lines, we find evidence that subjects in the high load treatment make worse choices than subjects in the low load treatment. Therefore the low quality searches do not fully explain the low quality choices. Our results suggest that cognition affects choice, even in our idealized choice setting. We also find evidence of choice overload even when the choice set is small and the objects are simple. Further, our experimental design permits a multinomial discrete choice analysis on choice among single-attribute objects with an objective value. The results of our analysis suggest that the errors in our data are better described as having a Gumbel distribution rather than a normal distribution. Finally, we observe the effects of limited cognition, consistent with memory decay and attention.
Mucins in inflammatory bowel diseases and colorectal cancer

The gastrointestinal tract is protected by a mucus barrier with both secreted and cell‐surface mucins contributing to the exclusion of luminal microbes and toxins. Alterations in the structure and/or quantity of mucins alter the barrier function of mucus and could play roles in initiating and maintaining mucosal inflammation in inflammatory bowel diseases (IBD), and in driving cancer development in the intestine. The aim of this review is to focus on the roles of the mucins in IBD. The polymorphisms of mucin genes that have been associated with susceptibility to IBD, and alterations in mucin expression as well as factors that regulate production of the mucins in IBD, are summarized. Data from animal models of intestinal inflammation, which support the importance of mucins in IBD and cancer development, are also discussed.
Identification of Amino Acids Involved in the Functional Interaction between DnaA Protein and Acidic Phospholipids*

DnaA protein, the initiator of chromosomal DNA replication in Escherichia coli, seems to be regulated through its binding to acidic phospholipids, such as cardiolipin. In our previous paper (Hase, M., Yoshimi, T., Ishikawa, Y., Ohba, A., Guo, L., Mima, S., Makise, M., Yamaguchi, Y., Tsuchiya, T., and Mizushima, T. (1998) J. Biol. Chem. 273, 28651–28656), we found that mutant DnaA protein (DnaA431), in which three basic amino acids (Arg360, Arg364, and Lys372) were mutated to acidic amino acids showed a decreased ability to interact with cardiolipin in vitro, suggesting that DnaA protein binds to cardiolipin through an ionic interaction. In this study, we construct three mutant dnaA genes each with a single mutation and examined the function of the mutant proteins in vitro and in vivo. All mutant proteins maintained activities for DNA replication and ATP binding. A mutant protein in which Lys372 was mutated to Glu showed the weakest interaction with cardiolipin among these three mutant proteins. Thus, Lys372 seems to play an important role in the interaction between DnaA protein and acidic phospholipids. Plasmid complementation analyses revealed that all these mutant proteins, including DnaA431 could function as an initiator for chromosomal DNA replication in vivo.
Mutations of the RTEL1 Helicase in a Hoyeraal‐Hreidarsson Syndrome Patient Highlight the Importance of the ARCH Domain

The DNA helicase RTEL1 participates in telomere maintenance and genome stability. Biallelic mutations in the RTEL1 gene account for the severe telomere biology disorder characteristic of the Hoyeraal‐Hreidarsson syndrome (HH). Here, we report a HH patient (P4) carrying two novel compound heterozygous mutations in RTEL1: a premature stop codon (c.949A>T, p.Lys317*) and an intronic deletion leading to an exon skipping and an in‐frame deletion of 25 amino‐acids (p.Ile398_Lys422). P4's cells exhibit short and dysfunctional telomeres similarly to other RTEL1‐deficient patients. 3D structure predictions indicated that the p.Ile398_Lys422 deletion affects a part of the helicase ARCH domain, which lines the pore formed with the core HD and the iron–sulfur cluster domains and is highly specific of sequences from the eukaryotic XPD family members.
An Integrated Model for Extracting Surface Deformation Components by PSI Time Series

The persistent scatterer interferometric synthetic aperture radar (PSI) has proven to be a powerful tool for monitoring surface deformation. However, the conventional deformation models cannot be fully adapted to analysis of the complicated deformation process. Taking into account seasonal response and tectonic movement, this letter presents an integrated deformation model for separating deformation components through PSI time series, thus obtaining the linear deformation rate, the deformation acceleration and the seasonal deformation amplitude at each PS. An iterative solution method is proposed to estimate the parameters in the integrated model. The experiments are carried out for subsidence detection over the northwestern part of Tianjin (China) by using the 40 high-resolution TerraSAR-X SAR images acquired between 2009 and 2010 and the ground truth data collected by precise leveling at seven benchmarks and six man-made corner reflectors. The testing results indicate that the integrated model has better adaptability to the subsidence process in the study area than the conventional models. The further analysis shows that the deformation results derived from the iterative solution are in better agreement with the ground truth data. These demonstrate that the proposed methodology is effective for monitoring the surface deformation with remarkable nonlinear property.
Calnexin expression does not enhance the generation of MHC class I‐peptide complexes

We investigated the requirement for calnexin in the biogenesis of MHC class I molecules. Mutant human cells lacking calnexin were infected with recombinant vaccinia viruses encoding mouse MHC class I molecules, K d , Kb , Kk , D d , Db , and Ld . Flow cytometry indicated that each of the six MHC class I allomorphs was transported to the cell surface at similar rates in calnexin‐deficient cells and transfectants expressing calnexin. For Kb and K d , the calnexin‐independent biogenesis occurred regardless of whether the MHC class I molecules contained human or mouse β2‐microglobulin. Also addressed was the effect of calnexin on the surface expression of Kb molecules bearing the immunodominant peptide from ovalbumin (OVA257 – 264 ). This was detected with a recently described monoclonal antibody specific for the Kb/peptide complex. Calnexin expression had no significant effect on the formation of Kb /peptide complexes generated from full‐length OVA, cytosolic OVA257 – 264 , or endoplasmic reticulum‐targeted OVA257 – 264 , which was expressed in the presence of the herpes simplex virus ICP47 protein to ensure detection of TAP‐independent peptide‐MHC class I complexes. Complementary results were obtained with TAP‐independent formation of K d /peptide complexes. These findings indicate that calnexin is not required for the efficient assembly of MHC class I molecules with TAP‐dependent or independent peptides.
A novel three-level zero-current-transition active neutral-point-clamped inverter

This paper extends the zero-current-transition concept to three-level active neutral-point-clamped inverter. The proposed soft-switching topology employs two auxiliary switches and one LC resonant tank to assist the main switching devices in one phase leg. The zero-current turning-off of all the main and auxiliary switching devices are achieved with voltage stress of all switching devices are clamped to half of the DC-link voltage. Meanwhile, The turning-on losses of main devices are reduced due to the limited current rising rate by the resonance as well as the reduced reverse recovery losses of main diodes. The operation principles are analyzed and simulation results verify the analysis.
Toward DNA-based security circuitry: First step — random number generation

DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. Our team investigates the implications of DNA-based circuit design in serving security applications. As an initial step, we develop a random number generation circuitry. A novel prototype schema employs solid-phase synthesis of oligonucleotides for random construction of DNA sequences. Temporary storage and retrieval is achieved through plasmid vectors.
Gender classification based on fuzzy SVM

Generalization ability is an important issue in gender classification. In this paper a gender classifier based on Fuzzy SVM (FSVM) is developed to improve the generalization ability. The fuzzy membership used in FSVM indicates the relativity of one personpsilas face with female/male faces set. This paper proposes a novel method of generating fuzzy membership function automatically based on Learning Vector Quantization (LVQ) learning process. The method doesnpsilat rely on the apriori information of data and has strong robustness to variations such as illumination, expression and so on. The gender classifier based on FSVM is evaluated on the FERET, CAS-PEAL, BUAA-IRIP face databases. The results show that the gender classifier presented in this paper can tolerate more variations and show good performance in generalization ability.
31P nuclear magnetic resonance study of the flavoprotein component of the Escherichia coli sulfite reductase.

SiR-FP60, the monomeric form of the Escherichia coli sulfite reductase flavoprotein component (SiR-FP), has been analysed by 31P-NMR spectroscopy. This protein was reported previously as a reliable simplified model for native SiR-FP [Zeghouf, M. , Fontecave, M. , Macherel, D. , & Covès, J. (1998) Biochemistry 37, 6117-6123]. SiR-FP60 was examined in its native form, as a complex with NADP+ and after monoelectronic reduction either with NADPH or dithionite. In these latter cases, the stabilized FMN semiquinone radical offers a natural and internal paramagnetic probe. The paramagnetic effect of added manganese was also studied. In each case, the NMR parameters were extracted from digitalized data by a deconvolution procedure and compared with those obtained previously with cytochrome P450 reductase. Evolution of the NMR parameters and of calculated relaxation rate constants upon biochemical modifications of SiR-FP60 led us to propose that the reactive center is more compact than the one of cytochrome P450 reductase, with the redox components, FMN, FAD and NADPH, in a tighter spatial arrangement, close to the protein surface. This underlies some subtle differences between the two proteins for which a very similar overall structure is likely considering their common genetic origin and common operating cycle.
Evaluation of e-prescribing in chain community pharmacy: best-practice recommendations.

OBJECTIVES To measure the attitudes and beliefs of community-based pharmacists and technicians toward electronic prescribing (e-prescribing) and the processing of e-prescriptions and to generate best-practice recommendations for changes to improve e-prescribing in the community setting. DESIGN Descriptive, nonexperimental, cross-sectional study. SETTING 422 chain community pharmacies in six states that met a minimum dispensing volume of five e-prescriptions per day. Data were collected between April and July 2006. PARTICIPANTS Pharmacists, technicians, and student interns. INTERVENTION Receiving, processing, and dispensing of e-prescriptions assessed via self-administered survey and follow-up interviews of key pharmacy operations and information technology management in each participating chain pharmacy organization. MAIN OUTCOME MEASURES Attitudes, beliefs, and satisfaction of pharmacy personnel regarding e-prescribing, compared with conventional prescribing, and recommendations for improving e-prescribing in the community practice setting. RESULTS 1,094 surveys were returned from pharmacy personnel practicing in 276 chain community pharmacies. Pharmacy personnel preferred e-prescriptions over conventional prescriptions on each of seven desired outcomes of care. Pharmacists were found to view e-prescribing more positively than technicians (P < 0.05) for its net effect on three key outcomes: patient safety, effectiveness of care, and efficiency of care. A total of 2,235 written comments were received on the returned surveys. Of these, 57% (1,277) mentioned negative features of e-prescribing, while 43% (958) noted positive features. Improved clarity and/or legibility of prescriptions was the most frequently cited advantage of e-prescribing, followed closely by improved speed or efficiency of processing. Prescribing errors were the most commonly cited negative feature of e-prescribing, particularly those stating a wrong drug or wrong directions. CONCLUSION Pharmacy personnel were generally satisfied with the current status of e-prescribing, but they also perceive key weaknesses in how it has been implemented in physicians' practices and their own organizations. A total of 11 best-practice recommendations are offered to improve e-prescribing in the chain community pharmacy setting.
The ABCA1 Transporter Modulates Late Endocytic Trafficking

We have previously established that the ABCA1 transporter, which plays a critical role in the lipidation of extracellular apolipoprotein acceptors, traffics between late endocytic vesicles and the cell surface (Neufeld, E. B., Remaley, A. T., Demosky, S. J., Jr., Stonik, J. A., Cooney, A. M., Comly, M., Dwyer, N. K., Zhang, M., Blanchette-Mackie, J., Santamarina-Fojo, S., and Brewer, H. B., Jr. (2001) J. Biol. Chem. 276, 27584-27590). The present study provides evidence that ABCA1 in late endocytic vesicles plays a role in cellular lipid efflux. Late endocytic trafficking was defective in Tangier disease fibroblasts that lack functional ABCA1. Consistent with a late endocytic protein trafficking defect, the hydrophobic amine U18666A retained NPC1 in abnormally tubulated, cholesterol-poor, Tangier disease late endosomes, rather than cholesterol-laden lysosomes, as in wild type fibroblasts. Consistent with a lipid trafficking defect, Tangier disease late endocytic vesicles accumulated both cholesterol and sphingomyelin and were immobilized in a perinuclear localization. The excess cholesterol in Tangier disease late endocytic vesicles retained massive amounts of NPC1, which traffics lysosomal cholesterol to other cellular sites. Exogenous apoA-I abrogated the cholesterol-induced retention of NPC1 in wild type but not in Tangier disease late endosomes. Adenovirally mediated ABCA1-GFP expression in Tangier disease fibroblasts corrected the late endocytic trafficking defects and restored apoA-I-mediated cholesterol efflux. ABCA1-GFP expression in wild type fibroblasts also reduced late endosome-associated NPC1, induced a marked uptake of fluorescent apoA-I into ABCA1-GFP-containing endosomes (that shuttled between late endosomes and the cell surface), and enhanced apoA-I-mediated cholesterol efflux. The combined results of this study suggest that ABCA1 converts pools of late endocytic lipids that retain NPC1 to pools that can associate with endocytosed apoA-I, and be released from the cell as nascent high density lipoprotein.