Miracle-dz/UniFAR-FTUs huggingface dataset:
Micromagnetic Simulation of Spin Valves with Synthetic Free and Pinned Layers and Detection of Magnetic Labels with AC Field

We present a micromagnetic simulation for detection of magnetic labels modulated by an ac magnetic field. As the sensing element, spin valves with synthetic ferrimagnetic (SF) free and pinned layers are optimized. At lower fields, the sensors with SF free layers show linear transfer curves, demonstrating a coherent switching due to the strong antiferromagnetic coupling inside the SF free layers. The sensor offset field can be reduced by tuning the effective thickness of SF free and pinned layers. Magnetic simulation for the detection of 250-nm magnetic labels with this sensor shows a linear giant magnetoresistive signal dependence on the number of particles.
Epitope analysis of a prostate-specific antigen (PSA) C-terminal-specific monoclonal antibody and new aspects for the discrepancy between equimolar and skewed PSA assays.

BACKGROUND Immunoassays to measure prostate-specific antigen (PSA) often give different values for the same patient samples, and the calibrators among commercial immunoassays are not interchangeable. We developed three novel assays to quantify the free and complexed forms of PSA in serum. METHODS We synthesized 46 peptides, which encompassed the entire PSA molecule, and determined the interactions between selected monoclonal antibodies (MAbs) and those peptides or the intact PSA molecule. RESULTS MAb PA313 did not cross-react with human glandular kallikrein (hK2), which has 78% amino acid homology to PSA. This MAb bound with KD = 40 nmol/L to the C-terminal peptide of PSA and distinguished between a synthetic peptide derived from PSA (PSA46A: NH2-C-R226KWIKDTIVANP237-COOH) that differed from one derived from hK2 (PSA46B: NH2-C-R226KWIKDTAANP237-COOH) by a single amino acid. Only the MAb combination of PA313/PA121 showed equimolar reactivity with PSA and with PSA complexed with alpha1-antichymotrypsin (PSA-ACT). The free form of PSA (F-PSA) was determined by MAbs PA313/FPA503, and the amount of complexed PSA (C-PSA) in PSA-ACT was determined by alphaACT/PA313. The total PSA (T-PSA) measured by either of the equimolar assays (PA313/PA121 or Tandem-R) was consistent with the sum of F-PSA and C-PSA. In contrast, T-PSA by a skewed assay (IMx) was higher than F-PSA + C-PSA when the ratio of F-PSA to T-PSA (F/T) was >0.15. T-PSA measured by IMx was nearly equal to F-PSA/0.55 + C-PSA. The coefficient 0.55 reflected different reactivities of the IMx assay with PSA-ACT and PSA. CONCLUSION The discrepancy between the values measured by equimolar and skewed assays depends on the ratio of free to total PSA in the sample.
Performance interactions between P-HTTP and TCP implementations

This document describes several performance problems resulting from interactions between implementations of persistent-HTTP (P-HTTP) and TCP. Two of these problems tie P-HTTP performance to TCP delayed-acknowledgments, thus adding up to 200ms to each P-HTTP transaction. A third results in multiple slow-starts per TCP connection. Unresolved, these problems result in P-HTTP transactions which are 14 times slower than standard HTTP and 20 times slower than potential P-HTTP over a 10 Mb/s Ethernet. We describe each problem and potential solutions. After implementing our solutions to two of the problems, we observe that P-HTTP performs better than HTTP on a local Ethernet. Although we observed these problems in specific implementations of HTTP and TCP (Apache-1.1b4 and SunOS 4.1.3, respectively), we believe that these problems occur more widely.
Neutralization Profiles of Sera from Human Immunodeficiency Virus (HIV)-Infected Individuals: Relationship to HIV Viral Load and CD4 Cell Count

ABSTRACT The relationship of the neutralizing activity (NA) profile of sera from human immunodeficiency virus (HIV)-infected individuals to the HIV viral load and the absolute CD4 count was examined. The NA of 24 serum samples against autologous isolates (AI) and HIV type 1 strain MN was examined. Three NA patterns were recognized. Nine sera neutralized both AI and MN (+/+), six sera neutralized MN but not AI (−/+), and nine sera failed to neutralize both AI and MN (−/−). The identification of the three neutralization patterns (+/+, −/+, and −/−) indicated that resistance to neutralization was progressive. A reciprocal relationship between the viral burden of the patients and the NA profiles was observed. The nine subjects with a −/− NA profile had a plasma viral load of ≥5 × 104 copies/ml and a cellular viral burden of ≥1,122 infectious units per million viable cells, which were significantly different from those of the other groups (P < 0.02). These patterns were independent of the phenotypic characteristics of the virus. Longitudinally, subjects with a −/− profile at baseline gained their HIV-specific NA by 24 weeks of antiretroviral therapy when this was associated with a ≥1-log10 decline in the plasma HIV viral load. The sera from week 24 from some patients were able to neutralize both the 24-week and the baseline dominant virus isolates. A change in CD4 cell count of 50 or more in either direction predicted a −/− or +/+ profile. The verification of the autologous NA profile might be important in selecting patients who may benefit from immune-based therapies involving neutralizing monoclonal antibodies.
Enhanced monitoring using PCA-based GLR fault detection and multiscale filtering

One of the most popular multivariate statistical methods used for data-based process monitoring is Principal Component Analysis (PCA). In the absence of a process model, PCA has been successfully used as a data-based FD technique for highly correlated process variables. Some of the PCA detection indices include the T2 or Q statistics, which have their advantages and disadvantages. When a process model is available, however, the generalized likelihood ratio (GLR) test, which is a statistical hypothesis testing method, has shown good fault detection abili ties. In this work, a PCA-based GLR fault detection algorithm is developed to exploit the advantages of the GLR test in the absence of a process model. In fact, PCA is used to provide a modeling framework for the develop fault detection algorithm. The PCA-based GLR fault detection algorithm provides optimal properties by maximizing the detection probability of faults for a given false alarm rate. However, the presence of measurement noise and modeling errors increase the rate of false alarms. Therefore, to further improve the quality of fault detection, multiscale filtering is utilized to filter the residuals obtained from the PCA model, which helps suppress the effect on errors, and thus decrease the false alarm rate. The proposed fault detection methodology is demonstrated through its application to monitor the ozone level in the Upper Normandy region, France, and it is shown to effectively reduce the rate of false alarms whilst retaining the capability of detecting process faults.
Evaluation of parotid gland function following intensity modulated radiation therapy for head and neck cancer.

PURPOSE This study was undertaken to determine the parotid gland tolerance dose levels following intensity modulated radiation therapy (IMRT) for treating patients who suffered with head and neck cancer. MATERIALS AND METHODS From February 2003 through June 2004, 34 head and neck patients with 6 months of follow-up were evaluated for xerostomia after being treated by IMRT. Their median age was 59 years (range: 29~78). Xerostomia was assessed using a 4-question xerostomia questionnaire score (XQS) and a test for the salivary flow rates (unstimulated and stimulated: USFR and SSFR, respectively). The patients were also given a validated LENT SOMA scale (LSS) questionnaire. Evaluations were performed before IMRT and at 1, 3 and 6 months after IMRT. RESULTS All 34 patients showed significant changes in the XQS, LSS and Salivary Flow rates (USFR and SSFR) after IMRT. No significant changes in the XQS or LSS were noted in 12 patients who received a total parotid mean dose of <or=3,100 cGy at 1, 3 and 6 months post-IMRT relative to the baseline values. However, for the 22 patients who received >3,100 cGy, significant increases in the XQS and LSS were observed. The USFR and SSFR from the parotid glands in 7 patients who received <or=2,750 cGy were significantly preserved at up to 6 months after IMRT. However, the USFR and SSFR in 27 patients who were treated with >2,750 cGy were significantly lower than the baseline values at all times after IMRT. CONCLUSION We suggest that the total parotid mean dose should be limited to <or=2,750 cGy to preserve the USFR and SSFR and so improve the subsequent quality of life.
Integrability of Lie brackets

In this paper we present the solution to a longstanding problem of differential geometry: Lie’s third theorem for Lie algebroids. We show that the integrability problem is controlled by two computable obstructions. As applications we derive, explain and improve the known integrability results, we establish integrability by local Lie groupoids, we clarify the smoothness of the Poisson sigma-model for Poisson manifolds, and we describe other geometrical applications.
Developmental Cycle and Genome Analysis of “Rubidus massiliensis,” a New Vermamoeba vermiformis Pathogen

The study of amoeba-associated Chlamydiae is a dynamic field in which new species are increasingly reported. In the present work, we characterized the developmental cycle and analyzed the genome of a new member of this group associated with Vermamoeba vermiformis, we propose to name “Rubidus massiliensis. ” This bacterium is well-adapted to its amoeba host and do not reside inside of inclusion vacuoles after phagocytosis. It has a developmental cycle typical of this family of bacteria, with a transition from condensed elementary bodies to hypodense replicative reticulate bodies. Multiplication occurs through binary fission of the reticulate bodies. The genome of “R. massiliensis” consists of a 2.8 Mbp chromosome and two plasmids (pRm1, pRm2) consisting of 39,075 bp and 80,897 bp, respectively, a feature that is unique within this group. The Re-analysis of the Chlamydiales genomes including the one of “R. massiliensis” slightly modified the previous phylogeny of the tlc gene encoding the ADP/ATP translocase. Our analysis suggested that the tlc gene could have been transferred to plant and algal plastids before the transfer to Rickettsiales, and that this gene was probably duplicated several times.
Tetrathiomolybdate is effective in a mouse model of arthritis.

OBJECTIVE To test for protective effects of therapy with tetrathiomolybdate, a copper-lowering drug, against collagen-induced arthritis in mice. METHODS Mice were injected with bovine collagen II, and limb joint swelling and erythema were scored. Tetrathiomolybdate treated mice received drug by oral gavage or in drinking water. Plasma ceruloplasmin was followed as a measure of body copper status, and maintained between 20 and 60% of baseline. Urine for isoprostane studies was collected in metabolic cages. At sacrifice, blood was collected for cytokine assays, and hind limbs fixed in formalin. RESULTS Tetrathiomolybdate strongly protected against the collagen-induced arthritis as reflected in scores of swelling and erythema, and as seen histologically. Further, tetrathiomolybdate strongly protected against the increase in urine isoprostanes (a marker of oxidant damage) seen in collagen treated controls. The drug also protected against the increase in interleukin 2, interleukin 1beta, and tumor necrosis factor-a levels seen in collagen treated controls. CONCLUSION Based on the positive results reported here, and the good safety profile of tetrathiomolybdate in human studies so far, a trial of tetrathiomolybdate in arthritis syndromes seems warranted.
Empirical Bayes conditional independence graphs for regulatory network recovery

MOTIVATION Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense regions of a network, a consequence of both computational complexity and unreliable parameter estimation when sample size is small. As a result, identification of hub genes is of special difficulty for these methods. METHODS We present a new algorithm, Empirical Light Mutual Min (ELMM), for large network reconstruction that has properties well suited for recovery of graphs with high-degree nodes. ELMM reconstructs the undirected graph of a regulatory network using empirical Bayes conditional independence testing with a heuristic relaxation of independence constraints in dense areas of the graph. This relaxation allows only one gene of a pair with a putative relation to be aware of the network connection, an approach that is aimed at easing multiple testing problems associated with recovering densely connected structures. RESULTS Using in silico data, we show that ELMM has better performance than commonly used network inference algorithms including GeneNet, ARACNE, FOCI, GENIE3 and GLASSO. We also apply ELMM to reconstruct a network among 5492 genes expressed in human lung airway epithelium of healthy non-smokers, healthy smokers and individuals with chronic obstructive pulmonary disease assayed using microarrays. The analysis identifies dense sub-networks that are consistent with known regulatory relationships in the lung airway and also suggests novel hub regulatory relationships among a number of genes that play roles in oxidative stress and secretion. AVAILABILITY AND IMPLEMENTATION Software for running ELMM is made available at http://mezeylab.cb. bscb.cornell.edu/Software.aspx. CONTACT ramimahdi@yahoo.com or jgm45@cornell.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Effect of community level intervention on nutritional status and feeding practices of under five children in Ile Ife, Nigeria

Introduction Childhood malnutrition remains a widespread problem in developing world like Nigeria. The country ranks second among the ten countries contributing to sixty percent of the world's wasted under-five children. Community Integrated Management of Childhood illness (CIMCI) is a programme that employs the use of community based counsellors to address child health and nutritional challenges of the under-five and has the potential to reduce the morbidity and mortality resulting from poor nutritional and feeding practices. The study assessed the effect of community level intervention on nutritional status and feeding practices of children in Ile-Ife, Nigeria. Methods A cross-sectional comparative study that employed the use of multi stage cluster sampling techniques in selecting 722 mothers of index under five children. The study was done in two Local Government Areas of Osun State, Nigeria. Quantitative techniques were used in data collection. Data analysis was done using SPSS version 20.0. Descriptive and bivariate analyses was performed. Results The two Local Government Area (LGA) did not differ significantly in their wealth index (p = 0.344). However, more children in the non-implementing LGA (16.1%) had low weight for age compared with 3.6% in the CIMCI implementing LGA (p = 0.000). A statistically significant difference exist in the MUAC measurement of children 12-23 months between the CIMCI implementing and non-implementing communities (p = 0.007). A higher percentage of caregivers (19.3%) introduced complementary feeding earlier than 6 months in the non-implementing area (p < 0.001). Conclusion Using community level nutritional counseling can greatly improve nutritional status and feeding practices of under five children.
Autism Spectrum Disorder: How Parents use Behavior Modification With Their Children

This qualitative research study explores how parents use behavior modifications with their children diagnosed with autism spectrum disorder. Seven participants, who are mothers of children diagnosed with autism, were interviewed for this study. This research found that essentially, parents use different techniques applied in various ways in specific situations based on the uniqueness of their child and the behaviors displayed. Several themes emerged from this study which includes: challenging behaviors, behavior modifications used, behavior modification becomes a way of life, the need to individualize behavior modifications, behavior modifications will change as the child changes, challenges of having a child with autism, coping strategies, advice to professionals, and finding the joys. The respondents displayed creativity and resiliency in their use of behavior modifications for their children. The challenging behaviors displayed varied among different types of behaviors such as sensory-related, verbally and physically aggressive conduct, lack of social skills, and obsessive behaviors. Additionally, each child had unique characteristics which required techniques to be tailored to him/her. This research study provides further implications to social work practice, in that autism spectrum disorder affects the entire family and supports and resources should encompass the system as a whole. Additionally, social workers must stay abreast on the newest research regarding autism spectrum disorder to provide the best practices. AUTISM SPECTRUM DISORDER 3
Simulating Crowd Movements Using Fine Grid Cellular Automata

Cellular automata models have been extensively used for simulating pedestrian movements. One weakness of this type of models, is the size of the cells which is mostly considered to be of the size of a pedestrian (i.e. 40cm*40cm or near to it). Each pedestrian stands in a single cell and during simulation time steps, transits to neighbouring cells. The size of the cells dictates discrete speed steps for pedestrians and chess like movements. A pedestrian could move one or more cells in a simulation time step or do not move at all. In order to have more smooth movement and different speeds for pedestrians (i.e. from different ages, physical and health status) we propose a finer grid cellular automata. We use this model to build a least effort cellular automata movement algorithm. The algorithm has been used in small scale movement layer of our multi-agent crowd simulation platform in order to allow more realistic simulations of crowd flows. A simple walkway scenario has been used to test the outcome of the model. Results of the simulation are reported in this paper.
Towards ground truthing observations in gray-box anomaly detection

Anomaly detection has been attracting interests from researchers due to its advantage of being able to detect zero-day exploits. A gray-box anomaly detector first observes benign executions of a computer program and then extracts reliable rules that govern the normal execution of the program. However, such observations from benign executions are not necessarily true evidences supporting the rules learned. For example, the observation that a file descriptor being equal to a socket descriptor should not be considered supporting a rule governing the two values to be the same. Ground truthing such observations is a difficult problem since it is not practical to analyze the semantics of every instruction in every program to be protected. In this paper, we propose using taint analysis to automatically help the ground truthing. Intuitively, the same taint source of two values provides ground truth of the data dependence. We implement a host-based anomaly detector with our proposed taint tracking and evaluate the accuracy of rules learned. Results show that we not only manage to filter out incorrect rules that would otherwise be learned (with high support and confidence), but manage recover good rules that are previously believed to be unreliable. We also present overheads of our system and time needed for training.
Evaluation of fracture resistance and failure risks of posterior partial coverage restorations.

STATEMENT OF PROBLEM Interest in posterior partial coverage restorations has increased because these restorations provide a more conservative treatment option than traditional cohesively based restorations; however, material selection has been a controversial topic in the current literature. PURPOSE To evaluate the fracture resistance of posterior partial coverage restorations restored with different materials, examine their stress distribution, and calculate failure risks using three-dimensional (3D) finite element analysis. METHODS Sixty extracted third molar teeth received 2-mm occlusal reduction maintaining cusp steepness of 45 degrees relative to occlusal surface. Teeth were allocated into four groups (N = 15) and restored with different materials: feldspathic ceramic, leucite-reinforced ceramic, lithium disilicate-reinforced ceramic (EMX), or indirect resin-based composite (COM). Restorations were luted with resin cement and submitted to compressive loads (Instron Corp, Norwood, MA, USA). The data were analyzed with one-way analysis of variance, followed by Tukey's HSD tests. A 3D finite element model of posterior partial coverage restorations was developed and validated. The model was used to approximate the maximum principal stress in each of the materials under a 100-N static vertical compression at the occlusal surface of the tooth. The risk of restoration failure was quantified and compared among the four different materials. RESULTS Group EMX had fracture resistance significantly higher than other testing groups. Group COM presented the most extensive fractures involving tooth and root structures. When compared with the other materials, group EMX exhibited higher stress concentration; however, the failure risk of the restoration was lower. CONCLUSIONS Fracture resistance and failure risks of posterior partial coverage restorations are significantly influenced by material selection. CLINICAL SIGNIFICANCE Many restorative materials have been advocated for partial coverage restorations. It is essential to ensure that restorative materials have sufficient strength to support occlusal forces and, in case of fracture, the remaining tooth structure is not compromised or placed at risk. This study revealed that all-ceramic materials had high incidences of fractures involving the materials themselves, whereas the predominant failure of resin-based composite involved the tooth structure in a catastrophic manner.
Efficient transduction and optogenetic stimulation of retinal bipolar cells by a synthetic adeno-associated virus capsid and promoter

In this report, we describe the development of a modified adeno‐associated virus (AAV) capsid and promoter for transduction of retinal ON‐bipolar cells. The bipolar cells, which are post‐synaptic to the photoreceptors, are important retinal targets for both basic and preclinical research. In particular, a therapeutic strategy under investigation for advanced forms of blindness involves using optogenetic molecules to render ON‐bipolar cells light‐sensitive. Currently, delivery of adequate levels of gene expression is a limiting step for this approach. The synthetic AAV capsid and promoter described here achieves high level of optogenetic transgene expression in ON‐bipolar cells. This evokes high‐frequency (~100 Hz) spiking responses in ganglion cells of previously blind, rd1, mice. Our vector is a promising vehicle for further development toward potential clinical use.