Miracle-dz/UniFAR-FTUs huggingface dataset:
AP1 Regulation of Proliferation and Initiation of Apoptosis in Erythropoietin-Dependent Erythroid Cells

ABSTRACT The transcription factor AP1 has been implicated in the induction of apoptosis in cells in response to stress factors and growth factor withdrawal. We report here that AP1 is necessary for the induction of apoptosis following hormone withdrawal in the erythropoietin (EPO)-dependent erythroid cell line HCD57. AP1 DNA binding activity increased upon withdrawal of HCD57 cells from EPO. A dominant negative AP1 mutant rendered these cells resistant to apoptosis induced by EPO withdrawal and blocked the downregulation of Bcl-XL. JunB is a major binding protein in the AP1 complex observed upon EPO withdrawal; JunB but not c-Jun was present in the AP1 complex 3 h after EPO withdrawal in HCD57 cells, with a concurrent increase injunB message and protein. Furthermore, analysis of AP1 DNA binding activity in an apoptosis-resistant subclone of HCD57 revealed a lack of induction in AP1 DNA binding activity and no change injunB mRNA levels upon EPO withdrawal. In addition, we determined that c-Jun and AP1 activities correlated with EPO-induced proliferation and/or protection from apoptosis. AP1 DNA binding activity increased over the first 3 h following EPO stimulation of HCD57 cells, and suppression of AP1 activity partially inhibited EPO-induced proliferation. c-Jun but not JunB was present in the AP1 complex 3 h after EPO addition. These results implicate AP1 in the regulation of proliferation and survival of erythroid cells and suggest that different AP1 factors may play distinct roles in both triggering apoptosis (JunB) and protecting erythroid cells from apoptosis (c-Jun).
Corneal angiogenic privilege: angiogenic and antiangiogenic factors in corneal avascularity, vasculogenesis, and wound healing (an American Ophthalmological Society thesis).

PURPOSE To determine the molecular basis of corneal avascularity during wound healing and determine the role of angiogenic and antiangiogenic factors in corneal vasculogenesis. METHODS The expression of proangiogenic factors (vascular endothelial growth factor [VEGF]; basic fibroblast growth factor [bFGF]; matrix metalloproteinase-2 [MMP-2]; and membrane-type 1-MMP [MT1-MMP]) and antiangiogenic factors (pigment epithelium-derived factor [PEDF]; angiostatin; restin; and endostatin) was analyzed in avascular corneas and in models of corneal neovascularization (bFGF pellet implantation, intrastromal injection of MT1-MMP cDNA, and surgically induced partial limbal deficiency). RESULTS Immunohistochemistry demonstrated the presence of antiangiogenic factors (PEDF, angiostatin, restin, and endostatin) and proangiogenic molecules (VEGF, bFGF, MMP-2, and MT1-MMP) in the cornea after wounding. Proangiogenic MMPs were upregulated in stromal fibroblasts in the vicinity of invading vessels following bFGF pellet implantation. Corneal neovascularization (NV) was also induced by intrastromal injection of MT1-MMP naked cDNA in conjunction with de-epithelialization. Partial limbal deficiency (HLD-) resulted in corneal NV in MMP-7 and MMP-3 knockout mice but not in wild type controls. CONCLUSIONS Corneal angiogenic privilege is an active process involving the production of antiangiogenic factors to counterbalance the proangiogenic factors (which are upregulated after wound healing even in the absence of new vessels). Our finding that the potent antiangiogenic factors, angiostatin and endostatin, are colocalized with several MMPs during wound healing suggests that MMPs may be involved in the elaboration of these antiangiogenic molecules by proteolytic processing of substrates within the cornea.
A semi‐parametric accelerated failure time cure model

A cure model is a useful approach for analysing failure time data in which some subjects could eventually experience, and others never experience, the event of interest. A cure model has two components: incidence which indicates whether the event could eventually occur and latency which denotes when the event will occur given the subject is susceptible to the event. In this paper, we propose a semi‐parametric cure model in which covariates can affect both the incidence and the latency. A logistic regression model is proposed for the incidence, and the latency is determined by an accelerated failure time regression model with unspecified error distribution. An EM algorithm is developed to fit the model. The procedure is applied to a data set of tonsil cancer patients treated with radiation therapy. Copyright © 2002 John Wiley & Sons, Ltd.
exl, an Exchangeable Genetic Island in Neisseria meningitidis

ABSTRACT The genetic structure and evolution of a novel exchangeable meningococcal genomic island was defined for the important human pathogen Neisseria meningitidis. In 125 meningococcal strains tested, one of three unrelated nucleotide sequences, designatedexl (exchangeable locus), was found between a gene required for heme utilization, hemO, andcol, encoding a putative Escherichia colicollagenase homologue. The 5′ boundary of each exlcassette was the stop codon of hemO, whereas the 3′ boundary was delineated by a 33-bp repeat containing neisserial uptake sequences located downstream of col. One of the three alternative exl cassettes contained the meningococcal hemoglobin receptor gene, hmbR (exl3). In other meningococcal strains, hmbR was absent from the genome and was replaced by either a nucleotide sequence containing a novel open reading frame, exl2, or a cassette containing exl3. The proteins encoded byexl2 and exl3 had no significant amino acid homology to HmbR but contained six motifs that are also present in the lipoprotein components of the lactoferrin (LbpB), transferrin (TbpB), and hemoglobin-haptoglobin (HpuA) uptake systems. To determine the evolutionary relationships among meningococci carryinghmbR, exl2, or exl3, isolates representing 92 electrophoretic types were examined.hmbR was found throughout the population structure ofN. meningitidis (genetic distance, >0.425), whereasexl2 and exl3 were found in clonal groups at genetic distances of <0.2. The commensal neisserial species were identified as reservoirs for all of the exl cassettes found in meningococci. The structure of these cassettes and their correlation with clonal groups emphasize the extensive gene pool and frequent horizontal DNA transfer events that contribute to the evolution and virulence of N. meningitidis.
Interspecific Variation in Critical Patch Size and Gap‐Crossing Ability as Determinants of Geographic Range Size Distributions

How biological processes such as reproduction and dispersal relate to the size of species’ geographic ranges constitutes a major challenge in spatial ecology and biogeography. Here we develop a spatially explicit theoretical framework that links fundamental population‐level ecological traits (e.g., rates of dispersal and population growth or decay) with landscape heterogeneity to derive estimates of species’ geographic range sizes and, further, distributions of geographic range sizes across species. Although local (patch‐scale) population dynamics in this model are completely deterministic, we consider a fragmented landscape of patches and gaps in which the spatial heterogeneity is itself stochastic. This stochastic spatial structure, which juxtaposes landscape‐level patch and gap characteristics against population‐level critical patch sizes and maximum gap‐crossing abilities, determines how far a novel species can spread from its evolutionary origin. Given reasonable assumptions about landscape structure and about the distribution of critical patch sizes and critical gap lengths among species, we obtain distributions of geographic range sizes that are qualitatively similar to those routinely found in nature (e.g., many species with small geographic ranges). Collectively, our results suggest that both interspecific differences in population‐level traits and the landscapes through which species spread help determine patterns of occupancy and geographic extent.
Sequence requirements for the export of the Plasmodium falciparum Maurer's clefts protein REX2

A short motif termed Plasmodium export element (PEXEL) or vacuolar targeting signal (VTS) characterizes Plasmodium proteins exported into the host cell. These proteins mediate host cell modifications essential for parasite survival and virulence. However, several PEXEL‐negative exported proteins indicate that the currently predicted malaria exportome is not complete and it is unknown whether and how these proteins relate to PEXEL‐positive export. Here we show that the N‐terminal 10 amino acids of the PEXEL‐negative exported protein REX2 (ring‐exported protein 2) are necessary for its targeting and that a single‐point mutation in this region abolishes export. Furthermore we show that the REX2 transmembrane domain is also essential for export and that together with the N‐terminal region it is sufficient to promote export of another protein. An N‐terminal region and the transmembrane domain of the unrelated PEXEL‐negative exported protein SBP1 (skeleton‐binding protein 1) can functionally replace the corresponding regions in REX2, suggesting that these sequence features are also present in other PEXEL‐negative exported proteins. Similar to PEXEL proteins we find that REX2 is processed, but in contrast, detect no evidence for N‐terminal acetylation.
Multidetector computed tomography in the preoperative workup of hilar cholangiocarcinoma

Hilar cholangiocarcinoma is associated with a dismal prognosis; however, curative resection may offer a chance of cure. Various factors should be considered in the surgical planning for curative resection. These factors include extent of bile duct involvement, relationship between portal vein and tumor involvement, diffuse hepatoduodenal ligament infiltration, vascular invasion, lymph node metastasis, peritoneal seeding, and hepatic volume. Using high-quality volume data from multidetector-row computed tomography (MDCT) and adequate postprocessing images, radiologists can provide various types of information, imperative for curative resection of a hilar cholangiocarcinoma. This review illustrates the role of MDCT in the preoperative workup of hilar cholangiocarcinoma.
On the realization of the optimum transmission strategy in MIMO systems

A method has been introduced to implement the optimum transmission strategy in MIMO systems. Based on the knowledge of the transmitting channel covariance matrix, a de-correlation transform has been designed to remove spatial correlation and antenna mutual coupling in the transmitting antennas. Simulation results show that if there is no correlation in the receiving array, this method can be used to obtain the i.i. d. channel capacity of a MIMO system. Results also reveal that when there is correlation in the receiving array, compensation is more effective with larger transmitting and receiving arrays. For transmitting and receiving arrays with a fixed number of elements, compensation is more effective when antenna separation is small.
Managing application compatibility during ETL tools and environment upgrades

Abstract Extract, transform and load (ETL) tools are software applications responsible for data extraction from multiple sources, cleansing, customisation and insertion into a data warehouse. ETL tools integrate data, which enables the building of the enterprise data warehouse. To meet different business requirements and in order to bring a system up to date or to improve its data integration capabilities, it is necessary to upgrade ETL tools periodically. This paper reviews issues related to software and tools upgrades in data warehousing environments. It reads as a research report for a practitioner audience. We propose the managing of ETL application compatibility during software upgrades through automated tools and processes. We will discuss the challenges involved in ETL application compatibility evaluation during ETL tool upgrade and propose step-by-step methods to approach this. We also share suggestions and recommendations for improvement realised through recent upgrade activities conducted in an enterprise data warehouse production environment.
Assessment of breast volume changes during human pregnancy using a three-dimensional surface assessment technique in the prospective CGATE study

Pregnancies and breastfeeding are two important protective factors concerning breast cancer risk. Breast volume and breast volume changes might be a breast phenotype that could be monitored during pregnancy and breastfeeding without ionizing radiation or expensive equipment. The aim of the present study was to document changes in breast volume during pregnancy prospectively. In the prospective Clinical Gravidity Association Trial and Evaluation programme, pregnant women were followed up prospectively from gestational week 12 to birth. Three-dimensional breast surface imaging and subsequent volume assessments were performed. Factors influencing breast volume at the end of the pregnancy were assessed using linear regression models. Breast volumes averaged 420 ml at the start of pregnancy and 516 ml at the end of pregnancy. The first, second and third quartiles of the volume increase were 41, 95 and 135 ml, respectively. Breast size increased on average by 96 ml, regardless of the initial breast volume. Breast volume increases during pregnancy, but not all womens’ breasts respond to pregnancy in the same way. Breast volume changes during pregnancy are an interesting phenotype that can be easily assessed in further studies to examine breast cancer risk.
Design and Optimization of FinFETs for Ultra-Low-Voltage Analog Applications

In this paper, we analyze the enormous potential of engineering source/drain extension (SDE) regions in FinFETs for ultra-low-voltage (ULV) analog applications. SDE region design can simultaneously improve two key analog figures of merit (FOM)-intrinsic dc gain (AVO) and cutoff frequency (fT) for 60 and 30 nm FinFETs operated at low drive current (Jds = 5 muA/mum). The improved AVO and fT are nearly twice compared to those of devices with abrupt SDE regions. The influence of the SDE region profile and its impact on analog FOM is extensively analyzed. Results show that SDE region optimization provides an additional degree of freedom apart from device parameters (fin width and aspect ratio) to design future nanoscale analog devices. The results are analyzed in terms of spacer-to-straggle ratio-a new design parameter for SDE engineered devices. This paper provides new opportunities for realizing future ULV/low-power analog design with FinFETs.
Peptidylglycine α‐amidating monooxygenase: A multifunctional protein with catalytic, processing, and routing domains

Peptide α‐amidation is a widespread, often essential posttranslational modification shared by many bioactive peptides and accomplished by the products of a single gene encoding a multifunctional protein, peptidylglycine α‐amidating monooxygenase (PAM). PAM has two catalytic domains that work sequentially to produce the final α‐amidated product peptide. Tissue‐specific alternative splicing can generate forms of PAM retaining or lacking a domain required for the posttranslational separation of the two catalytic activities by endoproteases found in neuroendocrine tissue. Tissue‐specific alternative splicing also governs the presence of a transmembrane domain and generation of integral membrane or soluble forms of PAM. The COOH‐terminal domain of the integral membrane PAM proteins contains routing information essential for the retrieval of PAM from the surface of endocrine and nonendocrine cells. Tissue‐specific endoproteolytic processing can generate soluble PAM proteins from integral membrane precursors. Soluble PAM proteins are rapidly secreted from stably transfected nonneuroendo‐crine cells but are stored in the regulated secretory granules characteristic of neurons and endocrine cells.
Brain activity in adolescent major depressive disorder before and after fluoxetine treatment.

OBJECTIVE Major depression in adolescents is a significant public health concern because of its frequency and severity. To examine the neurobiological basis of depression in this population, the authors studied functional activation characteristics of the brain before and after antidepressant treatment in antidepressant-naive depressed adolescents and healthy comparison subjects. METHOD Depressed (N=19) and healthy (N=21) adolescents, ages 11 to 18 years, underwent functional MRI assessment while viewing fearful and neutral facial expressions at baseline and again 8 weeks later. The depressed adolescents received 8 weeks of open-label fluoxetine treatment after their baseline scan. RESULTS Voxel-wise whole brain analyses showed that depressed youths have exaggerated brain activation compared with healthy comparison subjects in multiple regions, including the frontal, temporal, and limbic cortices. The 8 weeks of fluoxetine treatment normalized most of these regions of hyperactivity in the depressed group. Region-of-interest analyses of the areas involved in emotion processing indicated that before treatment, depressed youths had significantly greater activations to fearful relative to neutral facial expressions than did healthy comparison subjects in the amygdala, orbitofrontal cortex, and subgenual anterior cingulate cortex bilaterally. Fluoxetine treatment decreased activations in all three regions, as compared with the repeat scans of healthy comparison subjects. CONCLUSIONS While effective treatments are available, the impact of depression and its treatment on the brain in adolescents is understudied. This study confirms increases in brain activation in untreated depressed adolescents and demonstrates reductions in these aberrant activations with treatment.
Influence of the data codification when applying evolving classifiers to develop spoken dialog systems

In this paper we present a study of the influence of the representation of the data when applying evolving classifiers in a specific classification task. In particular, we consider an evolving classifier for the development of a spoken dialog system interacting in a practical domain. In order to conduct this study, we will first introduce an approach based on evolving fuzzy systems (EFS) which is employed to select the next system action of the dialog system. This classifier takes into account a set of evolving fuzzy rules which are automatically obtained using evolving systems. The reason for using EFS in this domain is that we can process streaming data on-line in real time and the structure and operation of the dialog model can dynamically change by considering the interaction of the dialog system with its users. Since we want to apply this evolving approach in a real domain, our proposal considers the data supplied by the user throughout the complete dialog history and the confidence measures provided by the recognition and understanding modules of the system. The paper is focused on the study of the influence of the codification of this input data to achieve the best performance of the proposed approach. To do this, we have completed this study for a real spoken dialog system providing railway information.
An Analysis of the Virginia Unemployment Compensation System

This report was written in response to a legislative directive specified by the Virginia General Assembly in House Joint Resolution (HJR) 611 to undertake a comprehensive review of the state's unemployment compensation system. Enacted during Virginia's 2001 legislative session, HJR 611 identified eight topics to be studied covering aspects of Unemployment Insurance (UI) benefit payments, financing and trust fund solvency. The analysis was to be undertaken in close consultation with the Virginia Employment Commission. This final report, a revision of an earlier draft report, responds to the HJR 611 legislative directive.
Econometrics of Asset Pricing: Methodological Review and Empirical Exercise

This review summarizes some of the methodology currently available for estimating and evaluating Beta and stochastic discount factor (SDF) models such as time-series regression, cross-sectional regression, Fama-MacBeth procedure, and the generalized method of moments (GMM). The Fama-French and Carhart models are estimated following this review.
Effects of work–family and family–work conflicts on flexible work arrangements demand: a gender role perspective

Abstract In recent years, a growing number of firms have adopted flexible work arrangements (FWAs) to help managers balance their work–family demands. Based on a sample of 1336 married managers in Korea, we found that work–family conflict increased the FWAs demand more for female managers than for male managers. When facing work–family conflict, the absence of family-supportive supervision increased the demand for FWAs, particularly among female managers. No such effect was found for family–work conflict. In addition, having a female supervisor led to an increased demand for FWAs from company managers. These results suggest that firms should pay close attention to gender difference and supervisory roles in predicting the demand for FWAs to alleviate work–family conflicts.
Dipeptidyl peptidase 4 inhibitors attenuates the decline of skeletal muscle mass in patients with type 2 diabetes

Activation of dipeptidyl peptidase 4 has been reported to be associated with impairment of insulin signalling in skeletal muscle, presumably leading to loss of muscle function. This study was aimed to investigate whether the use of dipeptidyl peptidase 4 inhibitors (DPP4i) could attenuate the progressive loss of muscle mass in patients with type 2 diabetes.
Using the rate of bacterial clearance determined by real-time polymerase chain reaction as a timely surrogate marker to evaluate the appropriateness of antibiotic usage in critical patients with Acinetobacter baumannii bacteremia*

Objective: Bacteremia caused by Acinetobacter baumannii is becoming more frequent among critically ill patients, and has been associated with high mortality and prolonged hospital stay. Multidrug resistance and delay in blood culture have been shown to be significant barriers to appropriate antibiotic treatment. Quantitative polymerase chain reaction assays were recently used to monitor bacterial loads; we hypothesized that the rate of bacterial clearance determined by quantitative polymerase chain reaction can be used as a timely surrogate marker to evaluate the appropriateness of antibiotic usage. Design: Prospective observational study. Setting: University hospital and research laboratory. Patients: Patients with culture-proven A. baumannii bacteremia in the intensive care units were prospectively enrolled from April 2008 to February 2009. Interventions: Plasmid Oxa-51/pCRII-TOPO, which contained a 431-bp fragment of the A. baumannii-specific Oxa-51 gene in a pCRII-TOPO vector, was used as the standard. Sequential bacterial DNA loads in the blood were measured by a quantitative polymerase chain reaction assay. Measurements and Main Results: We enrolled 51 patients with A. baumannii bacteremia, and examined 318 sequential whole blood samples. The initial mean bacterial load was 2.15 log copies/mL, and the rate of bacterial clearance was 0.088 log copies/mL/day. Multivariate linear regression using the generalized estimation equation approach revealed that the use of immunosuppressants was an independent predictor for slower bacterial clearance (coefficient, 1.116; p < .001), and appropriate antibiotic usage was an independent predictor for more rapid bacterial clearance (coefficient, −0.995; p < .001). Patients with a slower rate of bacterial clearance experienced higher in-hospital mortality (odds ratio, 2.323; p = .04) Conclusions: Immunosuppression and appropriate antibiotic usage were independent factors affecting the rate of clearance of A. baumannii bacteremia in critical patients. These findings highlight the importance of appropriate antibiotic usage and development of effective antibiotics against A. baumannii in an era of emerging antibiotic resistance. The rate of bacterial clearance could serve as a timely surrogate marker for evaluating the appropriateness of antibiotics.