Miracle-dz/UniFAR-FTUs huggingface dataset:
Neutrophil Elastase Mediates Innate Host Protection against Pseudomonas aeruginosa1

According to the widely accepted view, neutrophil elastase (NE), a neutrophil-specific serine protease, is a major contributor to Pseudomonas aeruginosa infection-associated host tissue inflammation and damage, which in severe cases can lead to death. Herein, we provide for the first time compelling evidence that the host rather employs NE to protect itself against P. aeruginosa infection. Using a clinically relevant model of pneumonia, targeted deficiency in NE increased the susceptibility of mice to P. aeruginosa. We found that NE was required for maximal intracellular killing of P. aeruginosa by neutrophils. In investigating the mechanism of NE-mediated killing of P. aeruginosa, we found that NE degraded the major outer membrane protein F, a protein with important functions, including porin activity, maintenance of structural integrity, and sensing of host immune system activation. Consistent with this, the use of an isogenic mutant deficient in outer membrane protein F negated the role of NE in host defense against P. aeruginosa infection.
Mucin Glycan Expression is Individual-Specific and Governed by the In Situ Microenvironment

Mucin glycosylation and individual susceptibility to disease is linked to the in situ microenvironment that de- termines features of the individual- and disease-specific glycans. In tissue culture paradigm, the in situ environment is not recreated and the synthesis of signature glycans vanishes. To evaluate the impact of the in situ-specific gastric epithelial environment on mucin glycan synthesis we investigated gastric mucin collected from 36 individual rats subjected to the same conditions and diet. The secretion collected during 3 hours of gastric perfusion contained from 67.7 to 1096.6 nmol mucin glycans and from 42.0 to 245.8 nmol glycosphingolipids (GSL). We identified four groups, each consisting of 6 animals, that contained O-glycans interacting with apical epithelial mucin receptor comprised of N-acetylgalactosamine (GalNAc), galactose (Gal), N-acetylglucosamine (GlcNAc) and fucose (Fuc ) in the ratio of 1:2:2:1, 1:2:3:1, 1:3:2:1, and 1:4:2:1. The remaining 10 rats produced glycans containing GalNAc, Gal, GlcNAc, Fuc in ratio 1:1:1:1, partially fucosy- lated glycans, and Fuc-free glycans consisting of GalNAc:Gal:GlcNAc in ratio of 1:4:2. The data support our hypothesis that individual-specific-gastric epithelial environment and individual-specific metabolome provide final imprint on the quantity, composition, and termination of mucin O-glycans.
Genetic isolation of fragmented populations is exacerbated by drift and selection

Reduced genetic variation at marker loci in small populations has been well documented, whereas the relationship between quantitative genetic variation and population size has attracted little empirical investigation. Here we demonstrate that both neutral and quantitative genetic variation are reduced in small populations of a fragmented plant metapopulation, and that both drift and selective change are enhanced in small populations. Measures of neutral genetic differentiation (FST) and quantitative genetic differentiation (QST) in two traits were higher among small demes, and QST between small populations exceeded that expected from drift alone. This suggests that fragmented populations experience both enhanced genetic drift and divergent selection on phenotypic traits, and that drift affects variation in both neutral markers and quantitative traits. These results highlight the need to integrate natural selection into conservation genetic theory, and suggests that small populations may represent reservoirs of genetic variation adaptive within a wide range of environments.
A generic shape descriptor using Bezier curves

Bezier curves are robust tool for a wide array of applications ranging from computer-aided design to calligraphic character, outlining and object shape description. In terms of the control point generation process, existing shape descriptor techniques that employ Bezier curves do not distinguish between regions where an object's shape changes rapidly and those where the change is more gradual or flat. This can lead to an erroneous shape description, particularly where there are significantly sharp changes in shape, such as at sharp corners. This paper presents a novel shape description algorithm called a generic shape descriptor using Bezier curves (SDBC), which defines a new strategy for Bezier control point generation by integrating domain specific information about the shape of an object in a particular region. The strategy also includes an improved dynamic fixed length coding scheme for control points. The SDBC framework has been rigorously tested upon a number of arbitrary shapes, and both quantitative and qualitative analyses have confirmed its superior performance in comparison with existing algorithms.
Small Vessel Disease and General Cognitive Function in Nondisabled Elderly: The LADIS Study

Background and Purpose— On cerebral magnetic resonance imaging (MRI), white matter hyperintensities (WMH) and lacunes are generally viewed as evidence of small vessel disease. The clinical significance of small vessel disease in terms of global cognitive function has as yet not been completely clarified. We investigated the independent contribution of WMH and lacunes to general cognitive function in a group of independently living elderly with varying degrees of small vessel disease. Methods— Data were drawn from the multicenter, multinational Leukokraurosis and Disability (LADIS) study. There were 633 independently living participants. General cognitive function was assessed using the Mini Mental State Examination (MMSE) and the modified Alzheimer Disease Assessment Scale (ADAS). On MRI, WMH was rated as mild, moderate, or severe. Lacunes were rated as none, few (1 to 3), or many (4 or more). Results— In the basic analysis, increasing severity of both WMH and lacunes was related to deteriorating score on the MMSE and ADAS. When WMH and lacunes were entered simultaneously, both MRI measures remained significantly associated with MMSE score. Increasing severity of WMH remained associated with ADAS score, whereas the association with lacunes became less prominent. These associations were independent of other risk factors for dementia, like education, depression, vascular risk factors, or stroke. Conclusion— We found WMH and lacunes to be independently associated with general cognitive function in a sample of independently living elderly. These results highlight the fact that WMH and lacunes should both be evaluated when assessing small vessel disease in relation to cognitive function.
CD40 Ligand-mediated Activation of the de Novo RelB NF-κB Synthesis Pathway in Transformed B Cells Promotes Rescue from Apoptosis*

CD40, a tumor necrosis factor receptor family member, is expressed on B lymphocytes. Interaction between CD40 and its ligand (CD40L), expressed on activated T lymphocytes, is critical for B cell survival. Here, we demonstrate that CD40 signals B cell survival in part via transcriptional activation of the RelB NF-κB subunit. CD40L treatment of chronic lymphocytic leukemia cells induced levels of relB mRNA. Similarly, CD40L-mediated rescue of WEHI 231 B lymphoma cells from apoptosis induced upon B cell receptor (surface IgM) engagement led to increased relB mRNA levels. Recently, we characterized a new de novo synthesis pathway for the RelB NF-κB subunit, induced by the cytomegalovirus IE1 protein, in which binding of p50/p65 NF-κB and c-Jun/Fra-2 AP-1 complexes to the relB promoter works in synergy to potently activate transcription (Wang, X., and Sonenshein, G. E. (2005) J. Virol. 79, 95–105). CD40L treatment of WEHI 231 cells caused induction of AP-1 family members Fra-2, c-Jun, JunD, and JunB. Cotransfection of Fra-2 with the Jun AP-1 subunits and p50/c-Rel NF-κB led to synergistic activation of the relB promoter. Ectopic expression of relB or RelB knockdown using small interfering RNA demonstrated the important role of this subunit in control of WEHI 231 cell survival and implicated activation of the anti-apoptotic factors Survivin and manganese superoxide dismutase. Thus, CD40 engagement of transformed B cells activates relB gene transcription via a process we have termed the de novo RelB synthesis pathway, which protects these cells from apoptosis.
Statistical evaluation of rough set dependency analysis

Rough set data analysis (RSDA) has recently become a frequently studied symbolic method in data mining. Among other things, it is being used for the extraction of rules from databases; it is, however, not clear from within the methods of rough set analysis, whether the extracted rules are valid.In this paper, we suggest to enhance RSDA by two simple statistical procedures, both based on randomization techniques, to evaluate the validity of prediction based on the approximation quality of attributes of rough set dependency analysis. The first procedure tests the casualness of a prediction to ensure that the prediction is not based on only a few (casual) observations. The second procedure tests the conditional casualness of an attribute within a prediction rule.The procedures are applied to three data sets, originally published in the context of rough set analysis. We argue that several claims of these analyses need to be modified because of lacking validity, and that other possibly significant results were overlooked.
Crystal Structure of an Invertebrate Caspase*

Caspases play an essential role in the execution of apoptosis. These cysteine proteases are highly conserved among metazoans and are translated as inactive zymogens, which are activated by proteolytic cleavages to generate the large and small subunits and remove the N-terminal prodomain. The 2.3 Å resolution crystal structure of active Sf-caspase-1, the principal effector caspase of the insect Spodoptera frugiperda, is presented here. The structure represents the first nonhuman caspase to be resolved. The structure of the cleaved and active protease was determined with the tetrapeptide inhibitor N-acetyl-Asp-Glu-Val-Asp-chloromethylketone covalently bonded to the active site cysteine. As expected, the overall fold of Sf-caspase-1 is exceedingly similar to that of the five active caspases from humans solved to date. The overall structure and active site arrangement of Sf-caspase-1 is most comparable with that of the human effector caspases, with which it shares highest sequence homology. The most prominent structural difference with Sf-caspase-1 is the position of the N-terminal region of the large subunit. Unlike the N terminus of human caspases, the N terminus of Sf-caspase-1 originates from the active site side where it interacts with active site loop L2 and then extends to the backside of the heterodimer. This unusual structural arrangement raises the possibility that the N-terminal prodomain plays a regulatory role during effector caspase activation or enzyme activity in insects.
Reconciling the influence of task-set switching and motor inhibition processes on stop signal after-effects

Executive response functions can be affected by preceding events, even if they are no longer associated with the current task at hand. For example, studies utilizing the stop signal task have reported slower response times to “GO” stimuli when the preceding trial involved the presentation of a “STOP” signal. However, the neural mechanisms that underlie this behavioral after-effect are unclear. To address this, behavioral and electroencephalography (EEG) measures were examined in 18 young adults (18–30 years) on “GO” trials following a previously “Successful Inhibition” trial (pSI), a previously “Failed Inhibition” trial (pFI), and a previous “GO” trial (pGO). Like previous research, slower response times were observed during both pSI and pFI trials (i.e., “GO” trials that were preceded by a successful and unsuccessful inhibition trial, respectively) compared to pGO trials (i.e., “GO” trials that were preceded by another “GO” trial). Interestingly, response time slowing was greater during pSI trials compared to pFI trials, suggesting executive control is influenced by both task set switching and persisting motor inhibition processes. Follow-up behavioral analyses indicated that these effects resulted from between-trial control adjustments rather than repetition priming effects. Analyses of inter-electrode coherence (IEC) and inter-trial coherence (ITC) indicated that both pSI and pFI trials showed greater phase synchrony during the inter-trial interval compared to pGO trials. Unlike the IEC findings, differential ITC was present within the beta and alpha frequency bands in line with the observed behavior (pSI > pFI > pGO), suggestive of more consistent phase synchrony involving motor inhibition processes during the ITI at a regional level. These findings suggest that between-trial control adjustments involved with task-set switching and motor inhibition processes influence subsequent performance, providing new insights into the dynamic nature of executive control.
The role of postoperative radiotherapy (PORT) in combined small cell lung cancer (C-SCLC)

Purpose To explore the value of radiotherapy in C-SCLC patients, especially in those receiving a radical resection. Results The differences of survivals between the postoperative radiotherapy (PORT) and non-PORT groups were not statistically significant. But analyzing the benefits in subgroups, PORT significantly improved OS (p = 0.015), DFS (p = 0.026), LRFS (p = 0.008) and DMFS (p = 0.030) in stage III patients. For the patients with N2 stage, all survivals of the PORT group were also statistically significantly higher than non-PORT group (p = 0.018, 0.032, 0.008, 0.042). Patients with more than 10% of metastatic lymph nodes could get a significant benefit survivals by receiving PORT (p = 0.033, 0.030, 0.025, 0.031). Having a systematic dissection of more than 17 lymph nodes was a subset which could get better OS and LRFS by receiving PORT (p = 0.045, 0.048). Methods Between Jan. 2004 to Dec. 2012, fifty-five patients diagnosed as C-SCLC after complete surgical resection in our center were retrospectively analyzed. The overall survival (OS), disease free survival (DFS), loco-regional recurrence free survival (LRFS), and distant metastasis free survival (DMFS) were calculated by Kaplan-Meier method. Conclusions PORT can significantly improve the survival of C-SCLC patients with resected pathological pN2 stage. For the patients with a large percent of metastatic lymph nodes, PORT can also improve survivals.
Development and Testing of the Helex Septal Occluder, a New Expanded Polytetrafluoroethylene Atrial Septal Defect Occlusion System

Background—A variety of transcatheter atrial septal defect (ASD) occluders are currently in use around the world. Although for the most part effective, all of these devices lack features that would be desirable in a “perfect” device. The Helex septal occluder is a new type of device designed to improve the results of transcatheter ASD closure. This study was designed to examine the effectiveness and safety of this occluder in an animal model. Methods and Results—The Helex was implanted into 24 dogs with surgically created ASDs. Procedural details focusing on deployment, removal, and early closure rates were examined. Follow-up consisted of sequential transesophageal echocardiography and fluoroscopy as well as epicardial contrast echocardiography and angiography at the time of death. Specimens were examined grossly and histologically, and devices were tested for metal fatigue. All animals had successful ASD closure. Implantation was uncomplicated (mean fluoroscopy time 11.7 minutes), and removal or repositioning was always possible. Closure rate as judged by transesophageal echocardiography was 88% initially and 100% at 2-week follow-up. Devices rapidly became infiltrated with connective tissue without inflammation and were endothelialized over time. There were no instances of thromboembolism. A single wire-frame fracture occurred secondary to a prototype delivery system malfunction. Conclusions—The Helex septal occluder proved safe and effective for ASD closure. Several advantages over currently available devices were evident in this model. Controlled prospective clinical trials are needed.
The role of ischemic preconditioning in the recruitment of rolling and adherent leukocytes in hepatic venules after ischemia/reperfusion.

BACKGROUND We have recently shown that hepatic ischemia/reperfusion (I/R) results in rolling and adherence of leukocytes in terminal hepatic venules (THV) followed by hepatic enzyme elevation and tissue destruction. The objective of this study was to determine the effect of ischemic preconditioning on the recruitment of leukocytes in THV after liver I/R. METHODS Left hepatic lobe ischemia was induced for 5 min (preconditioning) in anesthetized C57B1/6 mice followed by reperfusion for 10 min and then prolonged ischemia for 30 min. The number of rolling, saltating, and adherent leukocytes in THV was measured at 0.5, 2, 5, 12, and 24 h after reperfusion using intravital video microscopy. Matching sham groups were evaluated after 30 min of ischemia. RESULTS Hepatic I/R elicited significant increases in the number of rolling, saltating, and adherent leukocytes, with peak values observed at 30 min and 5 h after reperfusion. All of these responses were significantly attenuated in mice undergoing ischemic preconditioning. Rolling leukocytes in THV following I/R without preconditioning reached peak levels of 25.2 +/- 1.4 leuk/2 min (leukocytes/2 min) at 30 min reperfusion and 31.4 +/- 1.5 leuk/2 min at 5 h reperfusion. With ischemic preconditioning these values fell to 12.3 +/- 0.9 leuk/2 min and 14.4 +/- 1.0 leuk/2 min, respectively (P < 0.001). Similarly, adherent leukocytes in nonpreconditioned mice reached peak values of 4.8 +/- 1.3 leuk/2 min at 30 min reperfusion and 8.3 +/- 1.2 leuk/2 min at 5 h reperfusion compared with 2.0 +/- 1.5 leuk/2 min and 1.6 +/- 1.1 leuk/2 min in preconditioned mice, respectively (P < 0.001). CONCLUSION Ischemic preconditioning attenuates the initial events leading to leukocyte-mediated hepatic destruction following I/R injury. Delineating these mechanisms may play an important role in hepatic transplantation, resection, shock, and sepsis.
Incidence of needle tract seeding and responses of soft tissue metastasis by hepatocellular carcinoma postradiotherapy

Aim: To determine the incidence of needle tract seeding after fine needle aspiration (FNA) or percutaneous ethanol injection (PEI) and compare iatrogenic or spontaneous soft tissue metastasis (STM) by hepatocellular carcinoma (HCC) postradiotherapy (RT) in responses.
Comparison between two devices for measuring hip joint motions

Objective: To compare the reliability of measurements of hip motions obtained with two instruments, an electronic inclinometer and a two-arm goniometer, and to investigate whether the two instruments, and different body positions, produce the same measurement data. Methods: Maximal active and passive hip movements were measured simultaneously with both instruments, in nine subjects during 10 consecutive measurements at short intervals. Results: Intra-observer variability was lower with the inclinometer in measurements of passive hip rotations. The two instruments showed equal intra-observer variability for hip movements in general. The inclinometer showed lower inter-observer variability in the measurements of active internal rotation. More rotational movement was measured with the two-arm goniometer; more extension and flexion with the inclinometer. Also, more rotational movement was found in the prone position compared to sitting and supine positions. Conclusions: The inclinometer is more reliable in measurements of hip rotation. For hip movements in general the two-arm goniometer is just as accurate when used by only one observer. The two instruments, and some positions, are not interchangeable during consecutive measurements.
Properties and Wood Bonding Capacity of Nanoclay-Modified Urea and Melamine Formaldehyde Resins

Urea formaldehyde (UF) and melamine formaldehyde (MF) thermosetting resins were substituted with up to 6% nanoclay (organic modified Cloisite®30B and unmodified Nanofil® 116; Southern Clay Ltd, Austin, TX) and assessed for mixing and curing compatibility using X-ray diffraction, differential scanning calorimetry, wood lap-shear tests, and particleboard strength tests. Cloisite® 30B exfoliated fully in both resin types, whereas Nanofil® 116 showed increased spacing between platelets (intercalation) but not exfoliation. Nanoclays improved bonding strength of MF more than UF resin, and 2% nanoclay with a coupling agent in MF significantly enhanced particleboard bonding strength. Also, thickness swelling of particleboard in water decreased with up to 6% nanoclay. To decrease costs, MF resin could potentially be substituted by up to 6% nanoclay with no detrimental effect on properties.
Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.
Accommodating Innovation In A Juvenile Court

In an attempt to reduce the number of adjudicated juveniles being committed to the state for placement, the juvenile court in Wayne CountyMichigan implemented three intensive supervision programs to serve as alternatives to commitment. A four-year, randomized evaluation of the programs found them to be cost-effective. An analysis of court processes, however, suggested that the programs gradually came to supplement rather than to displace commitments as intended. The results of this study illustrate how juvenile justice organizations adapt to the presence of alternative programs in ways that dilute their impact.