Miracle-dz/UniFAR-FTUs huggingface dataset:
Methylcytosine and Normal Cytosine Deamination by the Foreign DNA Restriction Enzyme APOBEC3A*

Background: APOBEC3A is a myeloid-specific interferon-inducible DNA C to U deaminase implicated in innate immunity. Results: APOBEC3A also elicits MeC to T editing activity in vitro with deoxy-oligonucleotides and in vivo with transfected plasmids. Conclusion: APOBEC3A accommodates both normal and larger DNA cytosine substrates. Significance: The developmental specialization and broader substrate range of APOBEC3A may be an evolutionary adaptation for physiological function in foreign DNA restriction. Multiple studies have indicated that the TET oxidases and, more controversially, the activation-induced cytidine deaminase/APOBEC deaminases have the capacity to convert genomic DNA 5-methylcytosine (MeC) into altered nucleobases that provoke excision repair and culminate in the replacement of the original MeC with a normal cytosine (C). We show that human APOBEC3A (A3A) efficiently deaminates both MeC to thymine (T) and normal C to uracil (U) in single-stranded DNA substrates. In comparison, the related enzyme APOBEC3G (A3G) has undetectable MeC to T activity and 10-fold less C to U activity. Upon 100-fold induction of endogenous A3A by interferon, the MeC status of bulk chromosomal DNA is unaltered, whereas both MeC and C nucleobases in transfected plasmid DNA substrates are highly susceptible to editing. Knockdown experiments show that endogenous A3A is the source of both of these cellular DNA deaminase activities. This is the first evidence for nonchromosomal DNA MeC to T editing in human cells. These biochemical and cellular data combine to suggest a model in which the expanded substrate versatility of A3A may be an evolutionary adaptation that occurred to fortify its innate immune function in foreign DNA clearance by myeloid lineage cell types.
Pyrrolization and antioxidant function of proteins following oxidative stress.

The consequences of oxidative stress on microsomal proteins were analyzed by studying their pyrrolization and the antioxidative activity of the modified proteins produced. The microsomal system consisted of freshly prepared trout muscle microsomes, which were oxidized in the presence of 5 microM Cu(2+), 1 mM Fe(3+)/5 mM ascorbate, or 1 mM Cu(2+)/10 mM H(2)O(2). Pyrroles on proteins were detected by forming Ehrlich adducts with p-(dimethylamino)benzaldehyde and by determination of epsilon-N-pyrrolylnorleucine (Pnl) by capillary electrophoresis. Their antioxidative activity was studied by testing two model pyrrolized proteins (dimeric and monomeric modified bovine serum albumin: DBSA and MBSA, respectively), which were produced in the reaction of BSA and 4,5(E)-epoxy-2(E)-heptenal. These proteins were assayed at a concentration of 10-40 microg/mL, which was selected because at this concentration both DBSA and MBSA had a concentration of Pnl similar to the Pnl concentration produced in oxidized microsomes. Both DBSA and MBSA significantly (p < 0.05) protected against lipid peroxidation, assessed by the formation of thiobarbituric acid reactive substances (TBARS), and protein damage, evaluated by amino acid analysis, for the three systems assayed, and this protection was always higher than that exhibited by BSA, which was used as control. The order of effectiveness was DBSA > MBSA > BSA and was parallel to the Pnl content in the assayed proteins. These results suggest that antioxidative activity of BSA may also be related to its ability to react with lipid oxidation products and to produce modified BSA with antioxidative activity. This mechanism may also be contributing to the antioxidative activity exhibited by many proteins.
Environmental robust features for speech detection

In this paper, two novel features, Line Spectrum Center Range and Line Spectrum Flux, both derived from Line Spectrum Frequencies, are proposed to detect the presence of speech in various acoustic environments. Evaluation results using Fischer Discriminant Analysis and Scatter Matrices indicated that the new features excel the state-of-theart features. An environmental robust hybrid feature set including the proposed features, Normalized Energy Dynamic Range and Mel-Frequency Cepstrum Coefficients is further introduced. When evaluating the hybrid feature set on a Gaussian Mixture Model based classification engine, the results showed that the hybrid feature set outperformed MelFrequency Cepstrum Coefficients up to in terms of relative frame error rate.
System identification of neural mechanisms from trial-by-trial motor behaviour: modelling of learning, impairment and recovery

Abstract System identification is an engineering technique used to build mathematical models of dynamic systems from observed data. In neuroscience research, system identification has been used to adapt robotic devices for measurements and to apply perturbations. These techniques have been shown to be useful tools to investigate brain mechanisms of motor learning processes and motor dysfunctions. This paper reviews the application of system identification to motor behavioural data pertaining to the interruption of specific neural mechanisms. This system identification technique could reveal adaptation and generalisation functions in neural mechanisms for motor tasks to fit experimental data measured by the robotic devices in a discrete state-space model. When comparing constructed models between persons with neurological disabilities and healthy control subjects, system identification could be used to identify impaired abilities. Furthermore, a recent study indicated that such a discrete state-space model may predict recovery of motor function after stroke. Therefore, we suggest that the marriage between robotic devices and system identification will comprise a novel approach to clinical assessment and aid in the design of patient rehabilitation protocols.
MEF2C is required for the normal allocation of cells between the ventricular and sinoatrial precursors of the primary heart field

Targeted deletion of the mef2c gene results in a small left ventricle and complete loss of the right ventricle (Lin et al. [1997] Science 276:1404–1407). Absence of the right ventricle is from defective differentiation of cells from the secondary heart field. Our studies of the dysmorphogenesis of the left ventricle uncovered morphological and transcriptional abnormalities at the transition from the cardiac crescent to the linear‐tube stage heart. Use of the cgata6LacZ transgene demonstrated that lacZ‐positive cells, which normally mark the precursors to the atrioventricular canal and adjacent regions of the left ventricle and atria, remain in the sinoatrial region of the mutant. This, along with the absence of a morphologically distinct atrioventricular canal, indicates a misapportioning of cells between the inflow and outflow segments. The underlying genetic program was also affected with altered expression of mlc2a, mlc2v, and irx4 in outflow segment precursors of the primary heart field. In addition, the sinoatrial‐enriched transcription factor, tbx5, was ectopically expressed in the primitive ventricle and ventricle‐specific splicing of mef2b was lost, suggesting that the mutant ventricle had acquired atrial‐specific characteristics. Collectively, these results suggest a fundamental role of MEF2C in ventricular cardiomyocyte differentiation and apportioning of cells between inflow and outflow precursors in the primary heart field. Developmental Dynamics 235:1809–1821, 2006. © 2006 Wiley‐Liss, Inc.
Persistence and transferability of noroviruses on and between common surfaces and foods.

Human noroviruses (HuNoV) are the leading cause of foodborne disease, and poor personal hygiene practices of infected workers are the most common mode of contamination. The purpose of this study was to characterize the persistence and transferability of representative noroviruses Norwalk virus (NV), Snow Mountain virus (SMV), and murine norovirus 1 (MNV-1) on and between solid surfaces and foods. Changes in virus concentration on artificially inoculated solid surfaces (stainless steel, ceramic, and Formica) or lettuce were monitored over a period of 14 to 42 days. Virus transfer was evaluated from donor (solid surface) to recipient (food, e.g., lettuce and sliced turkey deli meat) for up to 2 h postinoculation. Viruses were recovered by elution and titered with reverse transcription quantitative PCR (RT-qPCR) and/or infectivity assay, as appropriate. Based on RTqPCR, the concentration of NV and SMV on surfaces dropped gradually over time, with an average reduction of 1.5 to 2.0 and 1.8 to 2.3 log, respectively, after 42 days, with no statistically significant differences by surface. When inoculated onto lettuce stored for 2 weeks at 4°C and room temperature, the titers of NV and SMV dropped by approximately 1.0 and 1.2 to 1.8 log, respectively. Comparatively, the RT-qPCR signal associated with purified HuNoV RNA placed on the same surfaces was more rapidly lost to degradation. Transfer efficiency ranged from 0 to 26 % for lettuce and from 55 to 95 % for sliced turkey deli meat, with statistically significant differences (P ≤ 0.05) in transferability as a function of contact pressure (100 and 1,000 g/9 cm(2)) and inoculum drying time. When similar experiments were done with MNV-1, infectious virus failed to be detected on solid surfaces after storage day 21, although the virus did persist on lettuce. This study provides much needed quantitative data for use in risk assessment efforts intended to characterize the transmission of HuNoV during food preparation and handling.
Numerical Simulation of Hypervelocity Impact FEM-SPH Algorithm Based on Large Deformation of Material

In this paper, we first discuss the research status and application progress of the finite element method and the smoothed particle method. By analyzing the advantages of the smoothed particle method and the finite element method, a new coupling algorithm, namely FEM-SPH algorithm, is proposed. By the method of comparison, it shows that finite element method and SPH method in the simulation of large deformation problems each have advantages and disadvantages, the finite element method smoothed particle coupling algorithm is effective to achieve the performance of high computational efficiency and can naturally simulate large deformation problems across. In the process of calculation, the large deformation unit can be freely into an algorithm to facilitate the calculation accuracy and efficiency of three methods of numerical simulation. Through the study found, FEM-SPH algorithm not only overcome the defect of smooth particle tensile instability, but also overcomes the problem of low efficiency of finite element computation. To further test the FEM-SPH algorithm has advantages in the practical engineering, we have carried out the actual test to the example of the super high speed collision, concluded that, since the target of most of the computational domain is always finite element, smoothed particle focused only in contact with the projectile and target of local area, particle number is not much, the whole calculation process just ten minutes, computational efficiency has been greatly improved, at the same time in the simulation of large deformation, the advantage is very obvious . This provides a criterion for the actual project, depending on the specific material deformation mode and choose a more appropriate conversion algorithm.
Intra-Extradural Plexiform Schwannoma of the Cervical Spine

Study Design. Case report. Objective. To describe the clinical and radiographic features of an extremely rare case with intra-extradural plexiform schwannoma of the cervical spine. Summary of Background Data. Plexiform schwannoma is a rare neurogenic tumor that predominantly occurs in the dermis and subcutis. Noncutaneous deep-seated lesions have rarely been described. No cases of intra-extradural plexiform schwannoma of the cervical spine have previously been reported. Methods. A 16-year-old boy presented with a 3-month history of left neck and shoulder angle pain, motor weakness of the left upper extremity, clumsiness of bilateral hands, and mild gait disturbance. Preoperative magnetic resonance imaging showed a multinodular inhomogeneous dumbbell-shaped tumor encroaching on the cord at C3–C4. T1-weighted imaging showed the tumor as inhomogeneous with slightly higher intensity than muscle. T2-weighted imaging demonstrated a multinodular inhomogeneous tumor with much higher intensity than muscle, and each nodule of the tumor displayed a peripheral rim of higher intensity and central relatively lower intensity. Results. Through hemi-laminectomy from C3–C4 and facetectomy of the left side of C3–C4, the intradural parts of the multinodular tumor were completely extirpated and extradural parts of the multinodular tumor were enucleated as much as possible. Gross examination of the tumor showed yellowish-white soft contents that were encapsulated and multilobulated. Histologic examination revealed benign schwannoma. After surgery, preoperative neurologic symptoms completely resolved. Conclusion. To the best of our knowledge, this is the first reported case of intra-extradural plexiform schwannoma. Careful magnetic resonance imaging might be helpful in suggesting this rare plexiform schwannoma before surgery.
An upper-body exoskeleton with a novel shoulder mechanism for assistive applications

The paper presents the mechatronic design of an upper-body exoskeleton. The problem of shoulder mechanism design is addressed to allow the exoskeleton able to match the motion of the human shoulder complex. A novel spherical mechanism that consists of two revolute joints connected together via a double parallelogram linkage (DPL) is analyzed and designed. With the new shoulder mechanism, a four-degree-of-freedom upper-body exoskeleton is designed and constructed. Human-robot interaction control with admittance controller is described and preliminary results are presented.
Histology and Histopatholog y Density of epidermal Langerhans cells in psoriasis patients treated with an aromatic retinoid ( RO 10-9359 ) . An immunoperoxidase study using anti-T 6 and anti-la monoclonal antibodies

Immunocytochemical techniques using antibodies to the specific T6 and Ia (Major Histocompability Complex, class 11, human HLA-Dr) antigens were used to determine the densities of epidermal Langerhans cells (LC) in psoriasis patients treated with the aromatic retinoid RO 10-9359. Fourteen patients were treated with the aromatic retinoid and were skin biopsied before, during and after therapy. Two psoriasis patients receiving PUVA (systemic 8-metoxypsoralen + UVA irradiation) were included in the study. The results showed an increase in LC numbers during aromatic retinoid administration, which coincided with an improvement in the clinical severity of the lesions. At the end of retinoid administration the LC numbers were similar to those found in the initial psoriatic plaques. The density of la + LC, in comparison with T6 + LC in the epidermis of psoriatic plaques were significantly different. Dendritic and non-dendritic I a+ . cells were also observed in the dermis of the plaques. Unlike aromatic retinoid treated patients, PUVA treated patients showed a decrease of both T6+ and Ia + epidermal LC by the middle of therapy, a total absence of immunoreaction by the end of therapy, and a return to normal skin values a few weeks after treatment. This immunocytochemical study helps in distinguishing between dendritic and other possible Iaexpressing cells from the infiltrate that may penetrate the epithelium. These results do not conclusively demonstrate the role of LC in the pathogenesis of psoriasis. Other factors, such
Monofunctional and Polyfunctional CD8+ T Cell Responses to Human Herpesvirus 8 Lytic and Latency Proteins

ABSTRACT Human herpesvirus 8 (HHV-8) is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. It is postulated that CD8+ T cell responses play an important role in controlling HHV-8 infection and preventing development of disease. In this study, we investigated monofunctional and polyfunctional CD8+ T cell responses to HHV-8 lytic proteins gB (glycoprotein B) and K8.1 and latency proteins LANA-1 (latency-associated nuclear antigen-1) and K12. On the basis of our previous findings that dendritic cells (DC) reveal major histocompatibility complex (MHC) class I epitopes in gB, we used a DC-based system to identify 2 novel epitopes in gB, 2 in K8.1, 5 in LANA-1, and 1 in K12. These new HHV-8 epitopes activated monofunctional and polyfunctional CD8+ T cells that produced various combinations of gamma interferon, interleukin 2, tumor necrosis factor alpha, macrophage inhibitory protein 1β, and cytotoxic degranulation marker CD107a in healthy HHV-8-seropositive individuals. We were also able to detect HHV-8-specific CD8+ T cells in peripheral blood samples using HLA A*0201 pentamer complexes for one gB epitope, one K8.1 epitope, two LANA-1 epitopes, and one K12 epitope. These immunogenic regions of viral lytic and latency proteins could be important in T cell control of HHV-8 infection.
Mining Popular Mobility Patterns from User GPS Trajectories

With the development of wireless communications and embedded systems technologies, many smartphones are equipped with a multitude of sensors such as GPS and powerful computational, storage and communication capabilities. By these smartphones, location-based services provide the potentialto understand people's mobility pattern at an unprecedented level. How to discover people's personal mobility patterns is key phase for location-based services to provide high-quality service. Therefore, we focus on mining popular mobility patterns from user GPS trajectories. Firstly, we propose a transform method that transforms a GPS trajectory into a sequence of POI(points of interest) based on the spatial and temporal property of GPS points. Then, we propose a periodic-frequent POI sets mining method to discover the POI sets which are not only occurring frequently, but also appearing periodically. Finally, experimental results show the efficiency and stability of the algorithm.
Emergency Preparedness for Pandemic Influenza

TARGET AUDIENCE This Continuing Medical Education activity is intended for physicians, nurses, and hospital administrators who are responsible for the development and implementation of hospital-based emergency preparedness plans. In addition, this article will be of interest to all health care workers (HCW) who are likely to provide medical care to patients infected with pandemic influenza, especially those who staff pediatric emergency departments (EDs).
Risk Factors Associated with Permanent Access-Site Infections in Chronic Hemodialysis Patients

Abstract Objective: To determine the epidemiological risk factors associated with permanent access-site (PAS) infection in a population of chronic hemodialysis patients. Design: Retrospective cohort analysis. Seiting: Hemodialysis unit of a 400-bed Department of Veterans' Affairs hospital. Results: A cohort of 94 males (1,316 patient months) was studied. Fifty-one PAS infections in 31 patients were observed. SiX patients had two PAS infections, four patients had three infections, and two patients had four infections. Twenty-nine of the 31 patients with PAS infections were bacteremic at least once. Univariate analysis identified seven factors significantly associated with PAS infection in this population: location of PAS other than forearm, type of vascular access (poletrafluoroethylene [PTFE] versus endogenous arteriovenous [AV] fistula), limited ambulatory status, residence in a nursing home, bacterial infection at a distant site, number of access-site revisions, and number of hospitalizations. In a logistic regression analysis, only graft type and number of PTFE graft revisions were associated independently with PAS infection. The odds ratio for PAS infection in PTFE grafts compared to endogenous AV fistula was 7.8; the odds ratio for PAS infection with each PTFE graft revision was 1.5. Conclusions: PAS infections were associated independently with the type of graft and the number of PTFE graft surgical revisions.
The neurotoxic effects of prenatal gabapentin and oxcarbazepine exposure on newborn rats

Abstract Aim: Teratogenicity is a problematic issue for pregnant women because of X-ray radiation, drugs, and genetic and unknown variables. First-generation antiepileptic drugs (AED) like valproic acid are well-known teratogens for developing fetuses. However, their usage is necessary in order to prevent maternal seizures. The underlying mechanism of birth defects associated with AED exposure remains unclear and information about the neurotoxic effects of prenatal exposure to AED is still limited. Oxcarbazepine (OXC) and gabapentin (GBP) are second-generation AED. It still remains unclear how much these drugs are safe during pregnancy. This study aimed to investigate whether any neurotoxic effect of OXC and GBP in utero exposure on the developing brain. Methods: Eighteen pregnant Wistar albino rats were divided into six groups. The first group was exposed to OXC at 100 mg/kg/day, the second to GBP at 50 mg/kg/day, and third to saline (0.9% NaCl) at 1.5 ml/day between the first and the fifth days of gestation. The same procedure was applied at the same dosages between the 6th and the 15th days of gestation for the 2nd three groups. Five female offspring (total n = 30, 45 days old) were taken from each group and stereological methods were applied in order to analyze the total and dopaminergic neuron number of the substantia nigra pars compacta (SNc). Conclusion: The result is that the OXC and GBP exposure at different gestational periods may not give rise to congenital malformation and it appears that the GBP exposure during the organogenesis period proliferatively affects the total number of neurons.
Prevalence of cardiovascular risk factors in adults with congenital heart disease

Background Empirical evidence indicates that patients with congenital cardiac anomalies may be prone to developing coronary heart disease. Although primary prevention of ischaemic heart disease in patients with congenital heart defects is important, data on the prevalence of cardiovascular risk factors in these patients are not available. The aims of this study are therefore to describe the prevalence of risk factors for coronary heart disease in a large sample of adults with congenital cardiac anomalies, and compare this with the prevalence in the general population. Design A retrospective analysis of computerized patient records. Methods At our outpatient clinic, all patients are examined by an advanced practice nurse and a congenital heart disease cardiologist. Data on smoking behaviour, sports participation, blood pressure, body mass index, and the diagnosis of diabetes are recorded systematically. Data on the general population were derived from national health surveys. Results In a 4-year period, we collected data on 1976 individual patients. Male patients had a significantly higher prevalence of smoking and elevated blood pressure, whereas women were less engaged in sports activities and were more often obese. In comparison with the general population, our patients reported less smoking and more participation in sports, but presented more often with hypertension or diabetes. Only 20.4% of men and 21.0% of women have a fully heart-healthy lifestyle, as they presented without any risk factor. Conclusion A substantial number of patients had one or more cardiovascular risk factors. Therefore, primary prevention by strengthening educational efforts becomes critically relevant in patients with congenital heart disease, to avoid the additional burden of coronary events in this growing population of patients.