Miracle-dz/UniFAR-FTUs huggingface dataset:
Characteristics of Airborne Pm2.5 and Pm2.5-10 in the Urban Environment of Kuala Lumpur

Gravimetric and elemental analyses were conducted at a site in Kuala Lumpur from 2008 to 2010, representing the local air quality of urban and traffic. Eighteen elements were detected by ED-XRF and was further analysed for enrichment factor and correlation study. About 19.7% elements were identified and detected in PM10, including 8.2% and 11.5% in fine and coarse fractions, respectively. Al was found predominant in coarse fraction. However its composition in PM2.5 was highly enriched pointed to some anthropogenic emission source. In fine particulates, the total mass was mostly dominated by Al, K, Mg and S. Those elements, probably from biomass burning accounted for more than 90% of total elemental detected in PM2.5.
Activation of TNF-a transcription utilizes distinct MAP kinase pathways in different macrophage populations

Stimulation of macrophages by lipopolysaccharide (LPS) leads to the rapid activation of MAP kinases (MAPK) and the subsequent induction of cytokine gene expression. We sought to determine whether LPS-inducible cytokine genes were differentially regulated in macrophages derived from different tissues. Our studies revealed that PD98059, an inhibitor of the extracellular-regulated kinase (ERK) pathway, blocked LPS-induced activation of tumor necrosis factor a (TNF-a) gene expression in a murine cell line derived from alveolar macrophages but not in a nonpulmonary macrophage cell line. These findings were confirmed using primary murine alveolar and peritoneal macrophages. This suggests that the TNF-a promoter contains MAPK-dependent and -independent regulatory elements that are used in a cell type-specific manner. We also found that differences in MAPK-regulated signaling were not mediated by NF-kB, LITAF, Egr-1, CREB, or ATF2/ c-Jun. Together, these studies demonstrate that transcriptional activation of the TNF-a gene requires the ERK signaling cascade in selected macrophage populations. J. Leukoc. Biol. 67: 885–893; 2000.
Morphology of bacterial granules developed in an upflow anaerobic acid reactor

Macro‐ and micro‐structures of granules, developed in an upflow anaerobic acid reactor, were examined by light and electron microscopy. Every granule was found to be white, soft and non‐spherical and had an open cavity at the centre. Scanning electron microscopy showed that the granules were composed of rod‐shaped bacteria, of different thicknesses and lengths, arranged in three distinct layers within the granules. Transmission electron microscopic analysis of ultra‐thin sections of granules, stained with Ruthenium Red, revealed the presence of extra‐cellular polymeric materials around the cells. Gram staining tests confirmed the presence of both Gram‐positive and Gram‐negative bacteria in the granules. The intertwined nature of the bacterial arrangement in the granules and the extracellular polymeric substance that encapsulated the cell colonies contributed to the structural stability of the granules.
Serum Dickkopf-1 as a Biomarker for the Diagnosis of Hepatocellular Carcinoma

Purpose Dickkopf-1 (DKK-1) is a Wnt/β-catenin signaling pathway inhibitor. We investigated whether DKK-1 is related to progression in hepatocellular carcinoma (HCC) cells and HCC patients. Materials and Methods In vitro reverse-transcription polymerase chain reaction (RT-PCR), wound healing assays, invasion assays, and ELISAs of patient serum samples were employed. The diagnostic accuracy of the serum DKK-1 ELISA was assessed using receiver operating characteristic (ROC) curves and area under ROC (AUC) analyses. Results RT-PCR showed high DKK-1 expression in Hep3B and low in 293 cells. Similarly, the secreted DKK-1 concentration in the culture media was high in Hep3B and low in 293 cells. Wound healing and invasion assays using 293, Huh7, and Hep3B cells showed that DKK-1 overexpression promoted cell migration and invasion, whereas DKK-1 knock-down inhibited them. When serum DKK-1 levels were assessed in 370 participants (217 with HCC and 153 without), it was significantly higher in HCC patients than in control groups (median 1.48 ng/mL vs. 0.90 ng/mL, p<0.001). The optimum DKK-1 cutoff level was 1.01 ng/mL (AUC=0.829; sensitivity 90.7%; specificity 62.0%). Although DKK-1 had a higher AUC than alpha-fetoprotein (AFP) and des-gamma-carboxy prothrombin (DCP) (AUC=0.829 vs. 0.794 and 0.815, respectively), they were statistically similar (all p>0.05). When three biomarkers were combined (DKK-1 plus AFP plus DCP), they showed significantly higher AUC (AUC=0.952) than single marker, DKK-1 plus AFP, or DKK-1 plus DCP (all p<0.001). Conclusion DKK-1 might be a key regulator in HCC progression and a potential therapeutic target in HCC. Serum DKK-1 could complement the diagnostic accuracy of AFP and DCP.
The ArsR protein is a trans‐acting regulatory protein

The arsR gene encodes the regulatory protein of the plasmid‐encoded arsenical resistance operon. A series of in‐frame fusions was constructed between the C‐terminally truncated arsR gene and the coding region for the mature form of β‐lactamase (blaM). Fusions containing most of the arsR gene were still inducible by arsenicals. Fusions containing less than 102 residues of the 117‐residue ArsR protein were constitutive. When a wild‐type arsR gene was placed in trans, the constitutive constructs were again inducible. The results demonstrate that the ArsR protein is a trans‐acting regulatory protein which controls its own expression.
A qualitative study of factors in nurses' and physicians' decision‐making related to family presence during resuscitation

AIMS AND OBJECTIVES To explore the similarities and differences in factors that influence nurses' and physicians' decision-making related to family presence during resuscitation. BACKGROUND Despite the growing acceptance of family presence during resuscitation worldwide, healthcare professionals continue to debate the risks and benefits of family presence. As many hospitals lack a policy to guide family presence during resuscitation, decisions are negotiated by resuscitation teams, families and patients in crisis situations. Research has not clarified the factors that influence the decision-making processes of nurses and physicians related to inviting family presence. This is the first study to elicit written data from healthcare professionals to explicate factors in decision-making about family presence. DESIGN Qualitative exploratory-descriptive. METHODS Convenience samples of registered nurses (n = 325) and acute care physicians (n = 193) from a Midwestern hospital in the United States of America handwrote responses to open-ended questions about family presence. Through thematic analysis, decision-making factors for physicians and nurses were identified and compared. RESULTS Physicians and nurses evaluated three similar factors and four differing factors when deciding to invite family presence during resuscitation. Furthermore, nurses and physicians weighted the factors differently. Physicians weighted most heavily the family's potential to disrupt life-saving efforts and compromise patient care and then the family's knowledge about resuscitations. Nurses heavily weighted the potential for the family to be traumatised, the potential for the family to disrupt the resuscitation, and possible family benefit. CONCLUSIONS Nurses and physicians considered both similar and different factors when deciding to invite family presence. Physicians focused on the patient primarily, while nurses focused on the patient, family and resuscitation team. RELEVANCE TO CLINICAL PRACTICE Knowledge of factors that influence the decision-making of interprofessional colleagues can improve collaboration and communication in crisis events of family presence during resuscitation.
Prognostic value of immunohistochemically identifiable tumor cells in lymph nodes of patients with completely resected esophageal cancer.

BACKGROUND Current methods of disease staging often fail to detect small numbers of tumor cells in lymph nodes. Metastatic relapse may arise from these few cells. METHODS We studied 1308 lymph nodes from 68 patients with esophageal cancer without overt metastases who had undergone radical en bloc esophagectomy. A total of 399 lymph nodes obtained from 68 patients were found to be free of tumor by routine histopathological analysis and were studied further for isolated tumor cells by immunohistochemical analysis with the monoclonal anti-epithelial-cell antibody Ber-EP4. This antibody did not stain lymph nodes from 24 control patients without carcinoma. RESULTS Of the 399 "tumor free" lymph nodes, 67 (17 percent), obtained from 42 of the 68 patients, contained Ber-EP4-positive tumor cells. Fifteen of 30 patients who were considered free of lymph-node metastases by histopathological analysis had such cells in their lymph nodes, and 5 of the 15 had small primary tumors. Ber-EP4-positive cells found in "tumor free" nodes were independently predictive of significantly reduced relapse-free survival (P=0.008) and overall survival (P=0.03). They predicted relapse both in patients without nodal metastases (P=0.01) and in those with regional lymph-node involvement (P=0.007). All 12 patients whose lymph nodes were negative on both histopathological and immunohistochemical analysis and who were available for follow-up survived without recurrence. The presence of micrometastatic tumor cells in bone marrow had no additional prognostic value. CONCLUSIONS Immunohistochemical examination of lymph nodes may improve the pathological staging of esophageal cancer.
2′, 3′‐cyclic nucleotide 3′‐phosphodiesterase cells derived from transplanted marrow stromal cells and host tissue contribute to perineurial compartment formation in injured rat spinal cord

Transdifferentiation of transplanted marrow stromal cells (MSCs) and reactive changes of glial cells in a completely transected rat spinal cord were examined. Marrow stromal cells exhibited 2′,3′‐cyclic nucleotide 3′‐phosphodiesterase (CNP) at the plasma membrane and this has allowed their identification after transplantation by immunoelectron microscopy. In the control rats, the lesion site showed activated microglia/neural macrophages and some elongated cells, whose cytoplasm was immunoreactive for CNP. Cells designated as CNP1 and apparently host‐derived expressed CXCR4. In experimental rats receiving MSCs transplantation, CNP1 cells were increased noticeably. This was coupled with the occurrence of a different subset of CNP cells whose plasma membrane was CNP‐immunoreactive and expressed CXCR4. These cells, designated as CNP2, enclosed both myelinated and unmyelinated neurites thus assuming a spatial configuration resembling that of Schwann cells. A remarkable feature was the extensive ramifications of CNP1 cells with long filopodia processes delineating the CNP2 cells and their associated neurites, forming many perineurial‐like compartments. Present results have shown that CNP2 cells considered to be MSCs‐derived can transform into cells resembling Schwann cells based on their spatial relation with the regenerating nerve fibers, whereas the CNP1 glial cells participate in formation of perineurial compartments, probably serving as conduits to guide the nerve fiber growth. The chemotactic migration of CNP cells either derived from host tissue or MSCs bearing CXCR4 may be attracted by stromal derived factor‐1α (SDF‐1α) produced locally. The coordinated cellular interaction between transplanted MSCs and local glial cells may promote the growth of nerve fibers through the lesion site. © 2006 Wiley‐Liss, Inc.
A C-V Method of Slow-Switching Interface Traps Identification in Silicon Carbide MOS Structures

A novel method based on the analysis of the C-V hysteresis change with increasing charge release time is proposed. The presence of a band of deep traps was demonstrated using this method in 3C-SiC samples. The same band of deep traps was also observed using photo-electric measurements of barrier height EBS in the same samples.
Epitope-Tagged Autotransporters as Single-Cell Reporters for Gene Expression by a Salmonella Typhimurium wbaP Mutant

Phenotypic diversity is an important trait of bacterial populations and can enhance fitness of the existing genotype in a given environment. To characterize different subpopulations, several studies have analyzed differential gene expression using fluorescent reporters. These studies visualized either single or multiple genes within single cells using different fluorescent proteins. However, variable maturation and folding kinetics of different fluorophores complicate the study of dynamics of gene expression. Here, we present a proof-of-principle study for an alternative gene expression system in a wbaP mutant of Salmonella Typhimurium (S. Tm) lacking the O-sidechain of the lipopolysaccharide. We employed the hemagglutinin (HA)-tagged inverse autotransporter invasin (invAHA) as a transcriptional reporter for the expression of the type three secretion system 1 (T1) in S. Tm. Using a two-reporter approach with GFP and the InvAHA in single cells, we verify that this reporter system can be used for T1 gene expression analysis, at least in strains lacking the O-antigen (wbaP), which are permissive for detection of the surface-exposed HA-epitope. When we placed the two reporters gfp and invAHA under the control of either one or two different promoters of the T1 regulon, we were able to show correlative expression of both reporters. We conclude that the invAHA reporter system is a suitable tool to analyze T1gene expression in S. Tm and propose its applicability as molecular tool for gene expression studies within single cells.
Experimental validation of a magnetorheological energy absorber design analysis

A key challenge when designing linear stroke magnetorheological energy absorbers for high-speed impact is that high piston speeds in linear stroke magnetorheological energy absorbers induce high Reynolds number flows in the magnetic valve of the magnetorheological energy absorber, so that achieving high controllable dynamic range can be a design challenge. So far, the research on magnetorheological energy absorbers has typically assumed that the off-state force increases linearly with piston velocity. But at the higher piston velocities occurring in impact events, the off-state damping exhibits nonlinear velocity squared damping effects. This problem was recognized in our prior work, where it was shown that minor losses are important contributing factors to off-state damping. In this study, a nonlinear analytical magnetorheological energy absorber model is developed based on a Bingham-plastic nonlinear flow model combined with velocity squared dependent minor loss factors. This refined model is denoted as the Bingham-plastic nonlinear flow model with minor losses. From this Bingham-plastic nonlinear flow model with minor losses, an effective design strategy is presented for conventional magnetorheological energy absorbers. The Bingham-plastic nonlinear flow model with minor losses is validated via computational fluid dynamics simulation, so that magnetorheological energy absorber performance can be analytically verified before being manufactured. The magnetorheological energy absorber is fabricated and tested up to an effective piston velocity of 5 m/s by using the high-speed drop tower facility at the GM R&D Center. Comparison of our analysis with measured data is conducted, and the effective design of the magnetorheological energy absorber using the Bingham-plastic nonlinear flow model with minor losses is validated.
Exploiting Shared Chinese Characters in Chinese Word Segmentation Optimization for Chinese-Japanese Machine Translation

Unknown words and word segmentation granularity are two main problems in Chinese word segmentation for ChineseJapanese Machine Translation (MT). In this paper, we propose an approach of exploiting common Chinese characters shared between Chinese and Japanese in Chinese word segmentation optimization for MT aiming to solve these problems. We augment the system dictionary of a Chinese segmenter by extracting Chinese lexicons from a parallel training corpus. In addition, we adjust the granularity of the training data for the Chinese segmenter to that of Japanese. Experimental results of Chinese-Japanese MT on a phrase-based SMT system show that our approach improves MT performance significantly.
A quantitative assessment of the accuracy and reliability of O-arm images for deep brain stimulation surgery.

BACKGROUND: Deep brain stimulation (DBS) surgery has an average accuracy of 2 to 3 mm (range, 0-6 mm). Intraoperative detection of track location may be useful in interpreting physiological results and thus limit the number of brain penetrations as well as decrease the incidence of reoperations. The O-arm has been used to identify the DBS lead position; however, early results have indicated a significant discrepancy with lead position on postoperative imaging. OBJECTIVE: This prospective study was conducted to determine the accuracy and reliability of fiducial and track localization and to assess the accuracy of O-arm image– based registration. The computed tomography (CT) image was considered the gold standard, and so for this study, the locations of all objects on the O-arm image were compared with their CT location. METHODS: Thirty-three DBS surgeries were performed using the O-arm to image each track with detailed analysis of fiducial and track localization accuracy. Twenty-one subsequent surgeries were performed using O-arm registration. Only the final lead position was assessed in these individuals. RESULTS: The measurement error of the system was 0.7 mm, with a maximum error of 1.9 mm. Twenty-two percent of the parallel tracks through the BenGun exceeded this error and demonstrated the ability of the O-arm to detect these skewed tracks. The accuracy of final lead position was 2.04 mm in procedures with registration based on an O-arm image. This was not significantly different from CT-based registration at 2.16 mm. CONCLUSION: The O-arm was able to detect skewed tracks and provide registration accuracy equivalent to a CT scan.
Elementary Mechanisms Producing Facilitation of Cav2.1 (P/Q-type) Channels

The regulation of CaV2.1 (P/Q-type) channels by calmodulin (CaM) showcases the powerful Ca2+ decoding capabilities of CaM in complex with the family of CaV1-2 Ca2+ channels. Throughout this family, CaM does not simply exert a binary on/off regulatory effect; rather, Ca2+ binding to either the C- or N-terminal lobe of CaM alone can selectively trigger a distinct form of channel modulation. Additionally, Ca2+ binding to the C-terminal lobe triggers regulation that appears preferentially responsive to local Ca2+ influx through the channel to which CaM is attached (local Ca2+ preference), whereas Ca2+ binding to the N-terminal lobe triggers modulation that favors activation via Ca2+ entry through channels at a distance (global Ca2+ preference). CaV2.1 channels fully exemplify these features; Ca2+ binding to the C-terminal lobe induces Ca2+-dependent facilitation of opening (CDF), whereas the N-terminal lobe yields Ca2+-dependent inactivation of opening (CDI). In mitigation of these interesting indications, support for this local/global Ca2+ selectivity has been based upon indirect inferences from macroscopic recordings of numerous channels. Nagging uncertainty has also remained as to whether CDF represents a relief of basal inhibition of channel open probability (P o) in the presence of external Ca2+, or an actual enhancement of P o over a normal baseline seen with Ba2+ as the charge carrier. To address these issues, we undertake the first extensive single-channel analysis of CaV2.1 channels with Ca2+ as charge carrier. A key outcome is that CDF persists at this level, while CDI is entirely lacking. This result directly upholds the local/global Ca2+ preference of the lobes of CaM, because only a local (but not global) Ca2+ signal is here present. Furthermore, direct single-channel determinations of P o and kinetic simulations demonstrate that CDF represents a genuine enhancement of open probability, without appreciable change of activation kinetics. This enhanced-opening mechanism suggests that the CDF evoked during action-potential trains would produce not only larger, but longer-lasting Ca2+ responses, an outcome with potential ramifications for short-term synaptic plasticity.
Cuticular hydrocarbon geographic variation among seven North American populations of Aedes albopictus (Diptera: Culicidae).

Cuticular hydrocarbons were used to differentiate among the following North American populations of Aedes albopictus: Chicago, Ill. ; Milford, Del. ; Jacksonville, Fla. ; San Antonio, Tex. ; New Orleans, La. ; Houston, Tex. ; and Lexington, Ky. Forty cuticular hydrocarbon peaks were identified from each population using gas chromatography electron impact-mass spectrometry: 16 n-alkanes, 21 monomethylalkanes, and 3 dimethylalkanes. Fourteen peaks occurred at equivalent chain lengths greater than 38.65 and consisted of complex mixtures of dimethyl- and trimethylalkanes. Quantitative analyses were performed on pooled samples of five females from each population using flame ionization gas chromatography. All populations contained the same cuticular hydrocarbons, but showed differences in percent composition. Five of seven populations were separable by discriminant analysis of hydrocarbon components.
The laminar origin and distribution of the crossed tectoreticular pathways

The superior colliculus is the source of a prominent descending pathway which crosses the midline in the mesencephalon and projects to the paramedian pontine reticular formation. The primary goal of the present study was to identify the cells in the superior colliculus of the grey squirrel which give rise to this pathway by using a combination of anterograde and retrograde tracing techniques. Results from the anterograde studies demonstrated the course and terminal distribution of this pathway and suggested that its laminar origin is the intermediate grey layer, stratum griseum intermediale. The retrograde studies were used to confirm the results of the anterograde experiments and to provide a more quantitative estimate of the laminar distribution of the cells which give rise to this pathway. In most cases, over 90% of the cells retrogradely labeled following injections of horseradish peroxidase along the course of this pathway were located in the intermediate grey lamina. This origin is in contrast to that of the ipsilateral tectoreticular pathway which originates primarily in stratum griseum profundum (Holcombe, V., and W. C. Hall (1981) Neuroscience 6: 255–260) and suggests that these two grey layers of the deep tectum are functionally distinct.