Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatic progenitor cells in liver cancers from Asian children

Background/Aims: Hepatoblastoma (HB) and hepatocellular carcinoma (HCC) are the two most common primary malignant liver tumours in children. Hepatic progenitor cells have been described and can be stained with K19, EpCAM and CD117. We investigated the morphology and staining patterns of primary liver tumours in Asian children.
A shape analysis framework for small animal phenotyping with application to mice with a targeted disruption of Hoxd11

This paper proposes the use of high-dimensional, point-based shape models for the study of phenotype, which offer some important advantages over traditional morphometries, including a more detailed representation of shape and a more systematic approach to shape statistics. Our approach allows for the analysis of shape at both global and local scales and can automatically extract lower- dimensional shape features useful for phenotypic characterization. We also demonstrate how covariates can be included in this framework. We apply the proposed modeling framework to a study of bone shape in mice with a targeted disruption of the Hoxd11 gene.
Investigation of oxidative stress during fracture healing in the rats

One of the most damaging effects of reactive oxygen species (ROS) is lipid peroxidation, the end‐product of which is malondialdehyde (MDA). This study was aimed to evaluate erythrocyte MDA levels during fracture healing in rats. Thirty male rats were used and the rats were divided into two groups to serve as controls and tests. Six rats were used as a control group that was not subject to fracture. The remaining 24 rats were divided into four groups and erythrocyte MDA levels were examined on days 5, 10, 20 and 30 post fracture. The right fibulas of rats were broken by manual angulation in the experimental group. The erythrocyte malondialdehyde level was measured in the experimental and control groups. The difference between malondialdehyde levels of control and experimental groups was statistically significant ( p < 0.05). Oxidative stress clearly increases during fracture healing in rats. Copyright © 2005 John Wiley & Sons, Ltd.
Impact of Rituximab on Immunoglobulin Concentrations and B Cell Numbers after Cyclophosphamide Treatment in Patients with ANCA-Associated Vasculitides

Objective To assess the impact of immunosuppressive therapy with cyclophosphamide (CYC) and rituximab (RTX) on serum immunoglobulin (Ig) concentrations and B lymphocyte counts in patients with ANCA-associated vasculitides (AAVs). Methods Retrospective analysis of Ig concentrations and peripheral B cell counts in 55 AAV patients. Results CYC treatment resulted in a decrease in Ig levels (median; interquartile range IQR) from IgG 12.8 g/L (8.15-15.45) to 9.17 g/L (8.04-9.90) (p = 0.002), IgM 1.05 g/L (0.70-1.41) to 0.83 g/L (0.60-1.17) (p = 0.046) and IgA 2.58 g/L (1.71-3.48) to 1.58 g/L (1-31-2.39) (p = 0.056) at a median follow-up time of 4 months. IgG remained significantly below the initial value at 14.5 months and 30 months analyses. Subsequent RTX treatment in patients that had previously received CYC resulted in a further decline in Ig levels from pre RTX IgG 9.84 g/L (8.71-11.60) to 7.11 g/L (5.75-8.77; p = 0.007), from pre RTX IgM 0.84 g/L (0.63-1.18) to 0.35 g/L (0.23-0.48; p<0.001) and from pre RTX IgA 2.03 g/L (1.37-2.50) to IgA 1.62 g/L (IQR 0.84-2.43; p = 0.365) 14 months after RTX. Treatment with RTX induced a complete depletion of B cells in all patients. After a median observation time of 20 months median B lymphocyte counts remained severely suppressed (4 B-cells/µl, 1.25-9.5, p<0.001). Seven patients (21%) that had been treated with CYC followed by RTX were started on Ig replacement because of severe bronchopulmonary infections and serum IgG concentrations below 5 g/L. Conclusions In patients with AAVs, treatment with CYC leads to a decline in immunoglobulin concentrations. A subsequent RTX therapy aggravates the decline in serum immunoglobulin concentrations and results in a profoundly delayed B cell repopulation. Surveying patients with AAVs post CYC and RTX treatment for serum immunoglobulin concentrations and persisting hypogammaglobulinemia is warranted.
Is Cardiovascular Reactivity Associated With Atherosclerosis Among Hypertensives?

Abstract—Exaggerated cardiovascular reactivity to behavioral challenges among otherwise healthy individuals has been associated with carotid atherosclerosis. We evaluated whether a similar relationship exists among hypertensives, who are at a heightened atherosclerotic risk. Untreated, hypertensive men (n=251; age range, 40 to 70 years; 197 white, 54 black) completed a standardized battery of behavioral challenges while their blood pressure responses to the battery were measured. Mean and maximum carotid intima-media thickness and the occurrence of carotid plaques were subsequently determined using B-mode ultrasonography. Although greater systolic and diastolic responses to the battery were associated with greater mean and maximum intima-media thickness in univariate analyses (P <0.01), only diastolic reactivity showed a unique association with mean and maximum carotid intima-media thickness after multivariate adjustment for age, race, socioeconomic status, smoking and alcohol use, body mass index, lipid profile, glucose and insulin concentrations, and resting blood pressure (P <0.05). Carotid plaque occurrence was associated with greater systolic reactivity (P =0.05) and was marginally associated with greater diastolic reactivity (P =0.07) in univariate analyses, but neither systolic nor diastolic reactivity was uniquely associated with the presence of carotid plaques after multivariate risk-factor adjustment. Among hypertensives, exaggerated behaviorally evoked cardiovascular reactivity appears to be uniquely associated with greater carotid intima-media thickness but not with carotid plaque occurrence.
New Model for the Genesis and Maturation of Viroplasms Induced by Fijiviruses in Insect Vector Cells

ABSTRACT Plant reoviruses are thought to replicate and assemble within cytoplasmic, nonmembranous structures called viroplasms. Here, we established continuous cell cultures of the white-backed planthopper (Sogatella furcifera Horváth) to investigate the mechanisms for the genesis and maturation of the viroplasm induced by Southern rice black-streaked dwarf virus (SRBSDV), a fijivirus in the family Reoviridae, during infection of its insect vector. Electron and confocal microscopy revealed that the viroplasm consisted of a granular region, where viral RNAs and nonstructural proteins P6 and P9-1 accumulated, and a filamentous region, where viral RNAs, progeny cores, viral particles, as well as nonstructural proteins P5 and P6 accumulated. Our results suggested that the filamentous viroplasm matrix was the site for the assembly of progeny virions. Because viral RNAs were produced by assembled core particles within the filamentous viroplasm matrix, we propose that these viral RNAs might be transported to the granular viroplasm matrix. P5 formed filamentous inclusions and P9-1 formed granular inclusions in the absence of viral infection, suggesting that the filamentous and granular viroplasm matrices were formed primarily by P5 and P9-1, respectively. P6 was apparently recruited in the whole viroplasm matrix by direct interaction with P9-1 and P5. Thus, the present results suggested that P5, P6, and P9-1 are collectively required for the genesis and maturation of the filamentous and granular viroplasm matrix induced by SRBSDV infection. Based on these results, we propose a new model to explain the genesis and maturation of the viroplasms induced by fijiviruses in insect vector cells.
Negative Feedback Regulation of NF-κB Action by CITED2 in the Nucleus

NF-κB is a family of important transcription factors that modulate immunity, development, inflammation, and cancer. The biological activity of NF-κB is subjected to various spatial and temporal regulations. Bioinformatics analysis predicts that CITED2 is topologically close to NF-κB in the protein interaction networks. In this study, we show that ectopic expression or knockdown of CITED2 attenuates or potentiates, respectively, the expression of NF-κB–responsive genes. Mechanistically, CITED2 constitutively localizes inside the nucleus and interacts specifically with the coactivator p300. This prevents p65 from binding to p300, impairs p65 acetylation, and attenuates p65 binding to its cognate promoters. Furthermore, LPS induces CITED2 expression via NF-κB in macrophages. CITED2 sensitizes cells to TNF-α–induced apoptosis. Collectively, this study identifies CITED2 as a novel regulator of NF-κB in the nucleus, which reveals a negative feedback mechanism for NF-κB signaling.
Evaluating Functional Activity in Older Thai Adults

&NA; The purpose of this study was to translate the original English version of the Self‐Efficacy and Outcome Expectations Scales for Exercise and Functional Activity and to establish their reliability in older Thai adults in geriatric rehabilitation. This study used a correlational design with repeated measures. Reliability of the Self‐Efficacy for Exercise Scale (SEES), the Self‐Efficacy for Functional Activity Scale (SEFAS), the Outcome Expectations for Exercise Scale (OEES), and the Outcome Expectations for Functional Activity Scale (OEFAS) developed by Resnick was measured in 20 older adults aged 60 years or older after hip or knee replacement or another orthopedic surgery of their lower extremity. All scales were translated into Thai and back translated into English according to the process described by Marin and Marin. The instruments were administered twice—the 1st and 2nd day in the participants' geriatric rehabilitation program (i.e., the 4th and 5th postoperative day). Results indicated that there was sufficient evidence for internal consistency of the SEES, SEFAS, OEES, and OEFAS with alpha coefficients of 0.84, 0.86, 0.70, and 0.86 respectively. Test‐retest reliability of the tools was also demonstrated with Spearman correlation coefficients of 0.84 for the SEES, 0.87 for the SEFAS, 0.61 for the OEES, and 0.54 for the OEFAS. The findings from this study provide important information for instrument adaptation and the applicability of these scales for further studies of older Thai adults.
Real-time FPGA architecture of extended linear convolution for digital image scaling

This paper presents a novel image interpolation method, extended linear interpolation, which is a low-cost architecture with the interpolation quality compatible to that of bi-cubic convolution interpolation. The architecture of reducing the computational complexity of generating weighting coefficients is proposed. Our proposed method provides a simple hardware architecture design, low computation cost and is easy to implement. Compared to the latest bi-cubic hardware design work, the architecture saves about 60% of hardware cost. The presented architecture is implemented on the Virtex-II FPGA has been successfully designed and implemented. The simulation results demonstrate that the high performance architecture of extended linear interpolation at 104 MHz with 379 LBs is able to process digital image scaling.
Simultaneous measurement of hole lifetime, hole mobility and bandgap narrowing in heavily doped n-type silicon

The hole diffusion length, hole lifetime, hole mobility, and hole equilibrium concentration in epitaxial heavily phosphorus-doped silicon have been measured by a combination of steady-state and transient techniques. Steady state measurements were performed on bipolar transistors in which the base was epitaxially grown. The transient measurement relied on the observation of the decay of the photoluminescence radiation after laser excitation. Significant findings are: 1) the hole mobility is about a factor of two larger in heavily doped n-type silicon than in p-type silicon; 2) the apparent bandgap narrowing is smaller than previously thought, with a value of about 90 meV at a doping level of 1020cm-3.
BEM simulations of Rayleigh wave propagation in media with microstructural effects: Application to long bones

Bone is a strongly heterogeneous natural composite with microstructure. Although the classical theory of linear elasticity has been largely used in bone ultrasonic studies, it cannot sufficiently describe the mechanical behavior of materials with microstructure. Furthermore, this theory predicts non-dispersive behavior of Rayleigh waves, which is in conflict with experimental observations. By using the simplest theory of gradient elasticity we recently demonstrated that bone's microstructure significantly affects the dispersion of classical Lamb modes. In this work, we investigate the effect of bone's microstructure on the propagation of Rayleigh waves by using the Boundary Element Method (BEM). We assume an isotropic semi-infinite space with mechanical properties equal to those of bone and microstructure. Microstructural effects are taken into account by introducing in the stress analysis the internal length scale parameters l1, l2, h1, h2. BEM computations are performed for various combinations of these parameters with values empirically chosen close to the osteon's size. The constants' values are also compared to those derived from closed form relations. The results made clear that bone's microstructure significantly affects Rayleigh wave dispersion.
Role of the Adapter Protein Abi1 in Actin-associated Signaling and Smooth Muscle Contraction*

Background: Neuronal Wiskott-Aldrich syndrome protein (N-WASP) regulates smooth muscle contraction by affecting actin polymerization. Results: Abi1 activated by c-Abl regulates N-WASP and smooth muscle contraction, and reciprocally controls c-Abl activation. Conclusion: The adapter protein Abi1 is essential for the regulation of actin cytoskeleton signaling and force development. Significance: The Abi1-mediated actin cytoskeleton process is a novel mechanism for the regulation of smooth muscle contraction. Actin filament polymerization plays a critical role in the regulation of smooth muscle contraction. However, our knowledge regarding modulation of the actin cytoskeleton in smooth muscle just begins to accumulate. In this study, stimulation with acetylcholine (ACh) induced an increase in the association of the adapter protein c-Abl interactor 1 (Abi1) with neuronal Wiskott-Aldrich syndrome protein (N-WASP) (an actin-regulatory protein) in smooth muscle cells/tissues. Furthermore, contractile stimulation activated N-WASP in live smooth muscle cells as evidenced by changes in fluorescence resonance energy transfer efficiency of an N-WASP sensor. Abi1 knockdown by lentivirus-mediated RNAi inhibited N-WASP activation, actin polymerization, and contraction in smooth muscle. However, Abi1 silencing did not affect myosin regulatory light chain phosphorylation at Ser-19 in smooth muscle. In addition, c-Abl tyrosine kinase and Crk-associated substrate (CAS) have been shown to regulate smooth muscle contraction. The interaction of Abi1 with c-Abl and CAS has not been investigated. Here, contractile activation induced formation of a multiprotein complex including c-Abl, CAS, and Abi1. Knockdown of c-Abl and CAS attenuated the activation of Abi1 during contractile activation. More importantly, Abi1 knockdown inhibited c-Abl phosphorylation at Tyr-412 and the interaction of c-Abl with CAS. These results suggest that Abi1 is an important component of the cellular process that regulates N-WASP activation, actin dynamics, and contraction in smooth muscle. Abi1 is activated by the c-Abl-CAS pathway, and Abi1 reciprocally controls the activation of its upstream regulator c-Abl.
Elucidation of the RamA Regulon in Klebsiella pneumoniae Reveals a Role in LPS Regulation

Klebsiella pneumoniae is a significant human pathogen, in part due to high rates of multidrug resistance. RamA is an intrinsic regulator in K. pneumoniae established to be important for the bacterial response to antimicrobial challenge; however, little is known about its possible wider regulatory role in this organism during infection. In this work, we demonstrate that RamA is a global transcriptional regulator that significantly perturbs the transcriptional landscape of K. pneumoniae, resulting in altered microbe-drug or microbe-host response. This is largely due to the direct regulation of 68 genes associated with a myriad of cellular functions. Importantly, RamA directly binds and activates the lpxC, lpxL-2 and lpxO genes associated with lipid A biosynthesis, thus resulting in modifications within the lipid A moiety of the lipopolysaccharide. RamA-mediated alterations decrease susceptibility to colistin E, polymyxin B and human cationic antimicrobial peptide LL-37. Increased RamA levels reduce K. pneumoniae adhesion and uptake into macrophages, which is supported by in vivo infection studies, that demonstrate increased systemic dissemination of ramA overexpressing K. pneumoniae. These data establish that RamA-mediated regulation directly perturbs microbial surface properties, including lipid A biosynthesis, which facilitate evasion from the innate host response. This highlights RamA as a global regulator that confers pathoadaptive phenotypes with implications for our understanding of the pathogenesis of Enterobacter, Salmonella and Citrobacter spp. that express orthologous RamA proteins.
What motivates use of community-based human immunodeficiency virus testing in rural South Africa?

Despite substantial progress in implementing HIV testing, challenges remain in achieving widespread uptake particularly in rural resource-limited settings. We sought to understand motivations for HIV testing in a community-based HIV testing programme in rural South Africa. We conducted a questionnaire survey in participants undergoing voluntary HIV testing within an ongoing community-based integrated HIV/tuberculosis intensive case finding programme at congregate rural settings. Participants responded to a six-item non-mutually exclusive motivations survey which included the topics of feeling ill, recent HIV exposure, risky lifestyle, illness in a family member, and pregnancy. Among 2068 respondents completing the survey, 1393 (67.4%) were women, median age was 40 years (IQR 19–56), and 1235 (59.7%) were first-time testers. Among all testers, 142 (6.9%) were HIV-positive with median CD4 count was 346 cells/mm3 (IQR 218–542). Community-based testing for HIV is acceptable and meets the needs of community members in rural South Africa. Motivations for HIV testing at the community level are complex and differ according to gender, age, site of community testing, and HIV status. These differences can be utilised to improve the focus and yield of community-based HIV screening.
A Hidden Markov, Multivariate Autoregressive (HMM-mAR) Network Framework for Analysis of Surface EMG (sEMG) Data

As the primary noninvasive means to assess muscle activation, the surface electromyogram (sEMG) is of central importance for the study of motor behavior in both clinical and biomedical applications. However, multivariate sEMG analysis is complicated by the fact that data recorded during dynamic contractions are inherently nonstationary. To model this nonstationarity and to determine the dynamic muscle activity patterns during reaching movements, we propose combining hidden Markov models (HMMs) and multivariate autoregressive (mAR) models into a joint HMM-mAR framework. We further propose constructing muscle networks statistically by performing a second level, group analysis on the subject-specific models. Network structural features are subsequently investigated as input features for the purpose of classification. The proposed approach was applied to real sEMG recordings collected from healthy and stroke subjects during reaching movements. When examining group muscle networks, we note that specific muscle connection patterns were selectively recruited during reaching movements and were differentially recruited after stroke compared to healthy subjects. As the analysis was performed on the raw data, the amplitude and the underlying ldquocarrier datardquo of sEMG signals, we notice that the HMM-mAR model fits the amplitude data well, but not the raw or carrier data. The proposed sEMG analysis framework represents a fundamental departure from existing methods where only the amplitude is typically analyzed or the mAR coefficients are directly used for classification. As the method may provide additional insights into motor control, it appears a promising approach warranting further study.
Bilateral Nerve Alterations in a Unilateral Experimental Neurotrophic Keratopathy Model: A Lateral Conjunctival Approach for Trigeminal Axotomy

To study bilateral nerve changes in a newly developed novel mouse model for neurotrophic keratopathy by approaching the trigeminal nerve from the lateral fornix. Surgical axotomy of the ciliary nerve of the trigeminal nerve was performed in adult BALB/c mice at the posterior sclera. Axotomized, contralateral, and sham-treated corneas were excised on post-operative days 1, 3, 5, 7 and 14 and immunofluorescence histochemistry was performed with anti-β-tubulin antibody to evaluate corneal nerve density. Blink reflex was evaluated using a nylon thread. The survival rate was 100% with minimal bleeding during axotomy and a surgical time of 8±0.5 minutes. The blink reflex was diminished at day 1 after axotomy, but remained intact in the contralateral eyes in all mice. The central and peripheral subbasal nerves were not detectable in the axotomized cornea at day 1 (p<0.001), compared to normal eyes (101.3±14.8 and 69.7±12.0 mm/mm2 centrally and peripherally). Interestingly, the subbasal nerve density in the contralateral non-surgical eyes also decreased significantly to 62.4±2.8 mm/mm2 in the center from day 1 (p<0.001), but did not change in the periphery (77.3±11.7 mm/mm2, P = 0.819). Our novel trigeminal axotomy mouse model is highly effective, less invasive, rapid, and has a high survival rate, demonstrating immediate loss of subbasal nerves in axotomized eyes and decreased subbasal nerves in contralateral eyes after unilateral axotomy. This model will allow investigating the effects of corneal nerve damage and serves as a new model for neurotrophic keratopathy.
Clinicopathologic, immunophenotypic, and molecular characterization of primary cutaneous follicular B-cell lymphoma.

OBJECTIVE To determine the clinicopathologic, immunophenotypic, and molecular characteristics of primary follicular cutaneous B-cell lymphoma (CBCL) as defined by the revised European-American lymphoma classification. DESIGN A retrospective survey of the medical records, an immunohistochemical study of archival biopsy specimens. and molecular studies of preserved DNA of all patients with follicle center lymphoma-follicular (FCL-F) primary CBCL from 1987 to 1997. SETTING A single-center outpatient specialty clinic at an academic medical center. PATIENTS Twenty-one patients (68% of all new primary CBCL cases), including 14 men and 7 women (age range, 33-88 years; mean, 55 years). RESULTS The head and neck region was the most frequent primary site. Following treatment, recurrences were relatively frequent, but the overall mortality rate during 1.0 to 11.3 years (mean, 6.3 years) of follow-up was 4.8%. Immunohistochemical analysis for B- and T-cell lineages was helpful in enhancing the folliclelike structures. CD10, bcl-2, and CD43 were expressed by the neoplastic cells in 9 (47%) of 19 cases, 4 (21%) of 19 cases, and 2 (13%) of 16 cases, respectively. Immunohistochemical detection of cytoplasmic immunoglobulin light chains, using steaming in EDTA as the antigen-retrieval technique, was successful in 12 (71%) of 17 cases. The Ig heavy-chain gene rearrangements, using the Southern blot technique, detected clonality in 17 (94%) of 18 cases. The bcl-2 gene rearrangements were detected in only 2 (13%) of 15 of the primary cutaneous FCL-F cases, compared with 9 (75%) of 12 of the primary nodal FCL-F cases (P =.002). CONCLUSIONS Primary cutaneous FCL-F is a relatively common subtype of CBCL, with a relatively indolent course. It has many features in common with primary nodal FCL-F, except for low rates of bcl-2 expression and bcl-2 gene rearrangements.