Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico analysis and modeling of ACP-MIP-PilQ chimeric antigen from Neisseria meningitidis serogroup B.

BACKGROUND Neisseria meningitidis, a life-threatening human pathogen with the potential to cause large epidemics, can be isolated from the nasopharynx of 5-15% of adults. The aim of the current study was to evaluate biophysical and biochemical properties and immunological aspects of chimeric acyl-carrier protein-macrophage infectivity potentiator protein-type IV pilus biogenesis protein antigen (ACP-MIP-PilQ) from N. meningitidis serogroup B strain. METHODS Biochemical properties and multiple alignments were predicted by appropriate web servers. Secondary molecular structures were predicted based on Chou and Fasman, Garnier-Osguthorpe-Robson, and Neural Network methods. Tertiary modeling elucidated conformational properties of the chimeric protein. Proteasome cleavage and transporter associated with antigen processing (TAP) binding sites, and T- and B-cell antigenic epitopes, were predicted using bioinformatic web servers. RESULTS Based on our in silico and immunoinformatics analyses, the ACP-MIP-PilQ protein (AMP) can induce high-level cross-strain bactericidal activity. In addition, several immune proteasomal cleavage sites were detected. The 22 epitopes associated with MHC class I and class II (DR) alleles were confirmed in the AMP. Thirty linear B-cell epitopes as antigenic regions were predicted from the full-length protein. CONCLUSION All predicted properties of the AMP indicate it could be a good candidate for further immunological in vitro and in vivo studies.
Interactions between the invasive brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), and entomopathogenic fungi

Title of Document: INTERACTIONS BETWEEN THE INVA SIVE BROWN MARMORATED STINK BUG, HALYOMORPHA HALYS (HEMIPTERA: PENTATOMIDAE), AND ENTOMOPATHOGENIC FUNGI Thomas John Pike, Master of Science 2014 Thesis Directed By: Dr. Paula Shrewsbury, Associate Professor Department of Entomology Brown marmorated stink bug, Halyomorpha halys, is an invasive stink bug native to Asia. It is a highly destructive pest in both agri cultural and ornamental systems. In an effort to identify a novel biological control, several strain s of entomopathogenic fungi were tested against brown marmorated stink bug nymphs and adults. Wild -type fungi were found to cause very low mortality in bioassays, as well as resulting in lit tle fungal growth or sporulation. The addition of diatomaceous earth and/or horticultural oil did not i crease mortality, nor did the use of transgenic fungi. To test the proposed mechanism o f brown marmorated stink bug's defense against fungal infection, trans-2-octenal and trans -2-decenal were bioassayed against several strains of entomopathogenic fungi. These compounds were found to inhibit fungal growth and prevent spore germination at low concentrations. R esults of an experiment to determine if brown marmorated stink bug responded to fungal exposure w e inconclusive. INTERACTIONS BETWEEN THE INVASIVE BROWN MARMORATED STINK BUG, HALYOMORPHA HALYS (HEMIPTERA: PENTATOMIDAE), AND ENTOMOPATHOGENIC FUNGI
The Effect of Social Support on Risky Sexual Behavior in Homeless Adolescent Youth.

This study examines the relationship between social support and youth's high-risk behaviors. The data were obtained from the Midwest Homeless and Runaway Adolescent Project (MHRAP) in 1996. In the Midwestern United States, this study examines the hypothesis that youth with high social support will have low sexual risk behaviors. The study found that youths who had someone to turn to, a greater number of close friends, and someone they could count on were less likely to engage in risky sexual behaviors. The implications of the findings are discussed.
White matter volume increase and minicolumns in autism

In Herbert and colleagues’ recent article, the authors report a localized white matter volume increase in both autism and developmental language disorder. According to the researchers, only the later myelinating outer white matter compartment was affected. Otherwise, no significant changes were reported for the inner white matter compartment containing longer bridging connections, for example, corpus callosum. The finding may account for the postnatal brain volume increase observed in the brains of autistic individuals. We have recently described minicolumnar abnormalities capable of explaining gray/white matter variations in the brains of autistic individuals. These abnormalities consisted in minicolumns being smaller but less compact in their cellular configuration. A study using the gray level index (GLI) has confirmed the results. If minicolumns are both narrower and sparser in their internal cell distribution, as in autism, there may be no overall difference in neuron density. Estimates of cortical interconnectivity for the human brain suggest that each module is connected to on the order of 10 other modules. If connectivity were fixed as brain size increased, then the number of connections would scale as the number of modular units squared, that is, doubling the number of minicolumns quadruples the number of fibers (Fig). Thus, a large percentage of additional brain volume would go to maintaining the connectivity. Hofman suggests that the actual scaling follows a 3⁄2-power law; that is, a fourfold increase in modular units requires an eightfold increase in fibers. Encephalization has seen a disproportionate increase in white matter relative to gray matter. The additional white matter primarily takes the form of short-range associational fibers, which make up the bulk of white matter devoted to intracortical connections. Researchers postulate that the spatial layout of the brain minimizes total connection costs. Long-range connectivity incurs the penalties of increased conduction time and requiring a large volume of metabolically active tissue. As the brain enlarges, the distance between cells and columns increases so that attempts to maintain connectivity results in signal transmission delays and inefficiency. Modules with short-range interconnections reduce both conduction time and metabolic requirements. Long commissural pathways, such as the corpus callosum, may better serve as an index of macrocolumnar rather than minicolumnar abnormalities. In a study of the visual cortex of cats, only a minority of callosal axons perform strict point-topoint mapping of retinotopically corresponding sites. Many of the callosal terminals had widespread arbors capable of influencing several minicolumns. Development of callosal axons in cat visual cortex shows that from the earliest stages callosal fibers grow into the gray matter in macrocolumnar-like bundles.
ORGB: Offset correction in RGB color space for illumination-robust image processing

Single materials have colors which form straight lines in RGB space. However, in severe shadow cases, those lines do not intersect the origin, which is inconsistent with the description of most literature. This paper is concerned with the detection and correction of the offset between the intersection and origin. First, we analyze the reason for forming that offset via an optical imaging model. Second, we present a simple and effective way to detect and remove the offset. The resulting images, named ORGB, have almost the same appearance as the original RGB images while are more illumination-robust for color space conversion. Besides, image processing using ORGB instead of RGB is free from the interference of shadows. Finally, the proposed offset correction method is applied to road detection task, improving the performance both in quantitative and qualitative evaluations.
Genital herpes simplex virus type 2 shedding is increased in HIV-infected women in Africa.

97 women of median age 26 years attending the National STD Reference Center in Bangui were enrolled during June-July 1998 in a study to assess the seroprevalence and genital shedding of herpes simplex virus type 2 (HSV-2) and which factors are associated with such shedding. 80% of the women were infected with HSV-2 genital shedding of the virus was observed among 32% 21% were infected with HIV and 87% were infected with some STD other than HIV. HSV-2 seroprevalence did not vary significantly by HIV serostatus. 13 of the 20 (65%) HIV-positive women were shedding HSV-2 compared with 18 of 77 (23%) HIV-negative women a significant difference which changed little after adjusting for age other STD or pregnancy status. In addition HIV-positive women shed significantly greater quantities of HSV-2 than did HIV-negative shedders. If HSV-2 shedding is associated with the increased shedding of HIV these study results would indicate that genital shedding may play an important role in HIV transmission in this part of Africa.
Changes in health professionals' knowledge, attitudes and practice following provision of educational resources about prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder.

We provided health professionals in Western Australia (WA) with educational resources about prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder and assessed changes in their knowledge, attitudes and practice concerning fetal alcohol syndrome (FAS) and alcohol consumption in pregnancy. Following our 2002 survey of health professionals in WA, we developed and distributed educational resources to 3348 health professionals in WA in 2007. Six months later we surveyed 1483 of these health professionals. Prevalence rate ratios [PRR] and 95% confidence intervals [CI] were calculated to compare 2007 results with results from the 2002 survey. Of the 1001 responding health professionals, 69.8% had seen the educational resources; of these 77.1% have used them and 48.5% said the resources had assisted them to change their practice or their intention to change their practice. Compared with 2002, there was an increase in the proportion who knew all the essential features of FAS from 11.7% to 15.8% [PRR 1.35; 95% CI 1.09, 1.67] and had diagnosed FAS, from 4.8% to 7.3% [PRR 1.52; 95% CI 1.08, 2.13]. In 2007, 98.1% of health professionals stated they would advise pregnant women to consider not drinking at all or advise them that no alcohol in pregnancy is the safest choice. Health professionals surveyed in 2007 have increased their knowledge, changed their attitudes and practice about FAS, and altered the advice they give to pregnant women about alcohol consumption since our survey in 2002. It is essential that we build on this change and continue to support health professionals' knowledge, attitudes and practice about the prevention of prenatal alcohol exposure and fetal alcohol spectrum disorder. The educational resources for health professionals may be ordered as hard copies and downloaded from the internet http://www.ichr. uwa.edu. au/alcoholandpregnancy.
Pore space reconstruction of vuggy carbonates using microtomography and multiple‐point statistics

To reconstruct complex porous media, such as carbonates, we propose a two‐step approach to combine different types of images: microtomography at the resolution of a few microns to resolve large pores and vugs, with statistically reconstructed high‐resolution images for smaller features. Two‐dimensional (2‐D) thin sections provide multiple‐point statistics which describe the statistical relation between multiple spatial locations that can be used to generate 3‐D images with accurate connectivity. These statistical reconstructions are combined with images directly measured by microtomography. The integrated method is tested on carbonates for which 3‐D images of disconnected vugs are captured, while 2‐D thin sections characterize the small‐scale structure. The integrated images have permeabilities computed using the lattice Boltzmann method that are similar to laboratory‐measured values.
MENGESTIMASI KEMAMPUAN PESERTA TES URAIAN MATEMATIKADENGAN PENDEKATAN TEORI RESPONS BUTIRDENGAN PENSKORAN POLITOMUSDENGAN GENERALIZED PARTIAL CREDIT MODEL

Dalam pelaksanaan tes uraian, penskoran biasanya dilakukan secara parsial berdasarkan langkah-langkah yang harus ditempuh untuk menjawab benar suatu butir soal. Penskoran dilakukan perlangkah dan skor perbutir diperoleh peserta diperoeh dengan menjumlah skor siswa tiap langkah, dan kemampuan diestimasi dengan skor mentah. Model penskoran seperti ini belum tentu tepat, karena tingkat kesulitan tiap langkah tidak diperhitungkan. Pendekatanl alternatif yang dapat digunakan yakni pendekatan teori respons butir untuk penskoran politomus, salah satunya dengan generalized partial credit model (GPCM). Pada artikel ini disajikan penskoran butir pada GPCM, model matematikanya, estimasi parameternya, dan estimasi kemampuan peserta disertai kasus dan pemanfaatan software Parscale dari SSi. Kata kunci: teori respons butir, generalized partial credit model
Quantifying Information Modification in Developing Neural Networks via Partial Information Decomposition

Information processing performed by any system can be conceptually decomposed into the transfer, storage and modification of information—an idea dating all the way back to the work of Alan Turing. However, formal information theoretic definitions until very recently were only available for information transfer and storage, not for modification. This has changed with the extension of Shannon information theory via the decomposition of the mutual information between inputs to and the output of a process into unique, shared and synergistic contributions from the inputs, called a partial information decomposition (PID). The synergistic contribution in particular has been identified as the basis for a definition of information modification. We here review the requirements for a functional definition of information modification in neuroscience, and apply a recently proposed measure of information modification to investigate the developmental trajectory of information modification in a culture of neurons vitro, using partial information decomposition. We found that modification rose with maturation, but ultimately collapsed when redundant information among neurons took over. This indicates that this particular developing neural system initially developed intricate processing capabilities, but ultimately displayed information processing that was highly similar across neurons, possibly due to a lack of external inputs. We close by pointing out the enormous promise PID and the analysis of information modification hold for the understanding of neural systems.
Making middleboxes someone else's problem: network processing as a cloud service

Modern enterprises almost ubiquitously deploy middlebox processing services to improve security and performance in their networks. Despite this, we find that today's middlebox infrastructure is expensive, complex to manage, and creates new failure modes for the networks that use them. Given the promise of cloud computing to decrease costs, ease management, and provide elasticity and fault-tolerance, we argue that middlebox processing can benefit from outsourcing the cloud. Arriving at a feasible implementation, however, is challenging due to the need to achieve functional equivalence with traditional middlebox deployments without sacrificing performance or increasing network complexity. In this paper, we motivate, design, and implement APLOMB, a practical service for outsourcing enterprise middlebox processing to the cloud. Our discussion of APLOMB is data-driven, guided by a survey of 57 enterprise networks, the first large-scale academic study of middlebox deployment. We show that APLOMB solves real problems faced by network administrators, can outsource over 90% of middlebox hardware in a typical large enterprise network, and, in a case study of a real enterprise, imposes an average latency penalty of 1.1ms and median bandwidth inflation of 3.8%.
Nutrition therapy in a pediatric intensive care unit: indications, monitoring, and complications.

BACKGROUND Nutrition therapy (NT) is essential for the care of critically ill children. Inadequate feeding leads to malnutrition and may increase the patient's risk of morbidity and mortality. The aim of this study was to describe the NT used in a tertiary pediatric intensive care unit (PICU). METHODS The authors evaluated NT administered to 90 consecutive patients who were hospitalized for 7 days in the PICU of Instituto da Criança, Hospital das Clínicas, Universidade de São Paulo, Brazil. NT was established according to the protocol provided by the institution's NT team. NT provided a balance of fluids and nutrients and was monitored with a weekly anthropometric nutrition assessment and an evaluation of complications. RESULTS NT was initiated, on average, within 72 hours of hospitalization. Most children (80%) received enteral nutrition (EN) therapy; of these, 35% were fed orally and the rest via nasogastric or postpyloric tube. There were gastrointestinal complications in patients (5%) who needed a postpyloric tube. Parenteral nutrition (PN) was used in only 10% of the cases, and the remaining 10% received mixed NT (EN + PN). The average calorie and protein intake was 82 kcal/kg and 2.7 g/kg per day. Arm circumference and triceps skinfold thickness decreased. CONCLUSIONS The use of EN was prevalent in the tertiary PICU, and few clinical complications occurred. There was no statistically significant change in most anthropometric indicators evaluated during hospitalization, which suggests that NT probably helped patients maintain their nutrition status.
Simpler Context-Dependent Logical Forms via Model Projections

We consider the task of learning a context-dependent mapping from utterances to denotations. With only denotations at training time, we must search over a combinatorially large space of logical forms, which is even larger with context-dependent utterances. To cope with this challenge, we perform successive projections of the full model onto simpler models that operate over equivalence classes of logical forms. Though less expressive, we find that these simpler models are much faster and can be surprisingly effective. Moreover, they can be used to bootstrap the full model. Finally, we collected three new context-dependent semantic parsing datasets, and develop a new left-to-right parser.
Modelling object perception in cortex: Hierarchical Bayesian networks and belief propagation

Hierarchical generative models and Bayesian belief propagation have been shown to provide a theoretical framework that can account for perceptual processes, including feedback modulation. The framework explains both psychophysical and physiological experimental data and maps well onto the hierarchical distributed cortical anatomy. The complexity required to model cortical processes makes inference, even using approximate methods, very computationally expensive. Thus, existing models are typically limited to tree-structured networks with no loops, use small toy examples or fail to account for certain perceptual aspects such as invariance to transformations or feedback reconstruction.
Functional Connectivity Changes in Resting-State EEG as Potential Biomarker for Amyotrophic Lateral Sclerosis

Background Amyotrophic Lateral Sclerosis (ALS) is heterogeneous and overlaps with frontotemporal dementia. Spectral EEG can predict damage in structural and functional networks in frontotemporal dementia but has never been applied to ALS. Methods 18 incident ALS patients with normal cognition and 17 age matched controls underwent 128 channel EEG and neuropsychology assessment. The EEG data was analyzed using FieldTrip software in MATLAB to calculate simple connectivity measures and scalp network measures. sLORETA was used in nodal analysis for source localization and same methods were applied as above to calculate nodal network measures. Graph theory measures were used to assess network integrity. Results Cross spectral density in alpha band was higher in patients. In ALS patients, increased degree values of the network nodes was noted in the central and frontal regions in the theta band across seven of the different connectivity maps (p<0.0005). Among patients, clustering coefficient in alpha and gamma bands was increased in all regions of the scalp and connectivity were significantly increased (p=0.02). Nodal network showed increased assortativity in alpha band in the patients group. The Clustering Coefficient in Partial Directed Connectivity (PDC) showed significantly higher values for patients in alpha, beta, gamma, theta and delta frequencies (p=0.05). Discussion There is increased connectivity in the fronto-central regions of the scalp and areas corresponding to Salience and Default Mode network in ALS, suggesting a pathologic disruption of neuronal networking in early disease states. Spectral EEG has potential utility as a biomarker in ALS.
Clinical evaluation of excitability measures in sensory nerve

A recently described method for recording multiple excitability parameters of human motor nerves has been adapted to the study of sensory nerves. The protocol measures stimulus–response behavior using two stimulus durations (from which the distribution of strength–duration time constants is estimated), threshold electrotonus to 100 ms polarizing currents, a current–threshold relationship (indicating inward and outward rectification), and the recovery of excitability following supramaximal activation. The method was tested on 50 healthy volunteers, stimulating the median nerve at the wrist and recording the antidromic compound sensory nerve action potential (SNAP) from digit 2. The excitability measurements were similar, where comparisons were possible, with published sensory nerve data, and confirmed differences from motor nerves, particularly in strength–duration behavior and recovery cycle, likely to reflect functional differences between sensory and motor nerves. Although slower than for motor nerves, the sensory nerve recordings were sufficiently quick (16 to 18 min) to allow them to be included in routine clinical studies. We propose that this method, which provides quite different and complementary information about nerve function to conventional conduction studies, provides a useful new approach for exploring the pathophysiology of sensory neuropathies. © 2001 John Wiley & Sons, Inc. Muscle Nerve 24: 883–892, 2001
Novel anti-tumor mechanism of galanin receptor type 2 in head and neck squamous cell carcinoma cells

Galanin and its receptors, GALR1 and GALR2, are known tumor suppressors and potential therapeutic targets in head and neck squamous cell carcinoma (HNSCC). Previously, we demonstrated that, in GALR1‐expressing HNSCC cells, the addition of galanin suppressed tumor proliferation via upregulation of ERK1/2 and cyclin‐dependent kinase inhibitors, whereas, in GALR2‐expressing cells, the addition of galanin not only suppressed proliferation, but also induced apoptosis. In this study, we first transduced HEp‐2 and KB cell lines using a recombinant adeno‐associated virus (rAAV)‐green fluorescent protein (GFP) vector and confirmed a high GFP expression rate (>90%) in both cell lines at the standard vector dose. Next, we demonstrated that GALR2 expression in the presence of galanin suppressed cell viability to 40–60% after 72 h in both cell lines. Additionally, the annexin V‐positive rate and sub‐G0/G1 phase population were significantly elevated in HEp‐2 cells (mock vs GALR2: 12.3 vs 25.0% (P < 0.01) and 9.1 vs 32.0% (P < 0.05), respectively) after 48 h. These changes were also observed in KB cells, although to a lesser extent. Furthermore, in HEp‐2 cells, GALR2‐mediated apoptosis was caspase‐independent, involving downregulation of ERK1/2, followed by induction of the pro‐apoptotic Bcl‐2 protein, Bim. These results illustrate that transient GALR2 expression in the presence of galanin induces apoptosis via diverse pathways and serves as a platform for suicide gene therapy against HNSCC.