Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrix Metalloproteinase-1 Is Regulated in Tuberculosis by a p38 MAPK-Dependent, p-Aminosalicylic Acid-Sensitive Signaling Cascade1

Mycobacterium tuberculosis (M. tb) must cause lung disease to spread. Matrix metalloproteinases (MMPs) degrade the extracellular matrix and are implicated in tuberculosis-driven tissue destruction. We investigated signaling pathways regulating macrophage MMP-1 and -7 in human pulmonary tuberculosis and examine the hypothesis that the antimycobacterial drug p-aminosalicylic acid acts by inhibiting such pathways. In primary human macrophages, M. tb up-regulates gene expression and secretion of MMP-1 (interstitial collagenase) and MMP-7 (matrilysin). In tuberculosis patients, immunohistochemical analysis of lung biopsies demonstrates that p38 MAPK is phosphorylated in macrophages surrounding granulomas. In vitro, M. tb drives p38 phosphorylation. p38 inhibition suppresses M. tb-dependent MMP-1 secretion by 57.8% and concurrently increases secretion of its specific inhibitor TIMP-1 by 243.7%, demonstrating that p38 activity regulates matrix degradation by macrophages. p38 signals downstream to the cyclooxygenase 2/PGE2 pathway. p-Aminosalicyclic acid, an agent used to treat drug-resistant tuberculosis, inhibits M. tb-driven MMP-1 but not MMP-7 gene expression and secretion. PAS acts by blocking PGE2 production without affecting M. tb growth. In summary, p-aminosalicyclic acid decreases MMP-1 activity by inhibiting a p38 MAPK-PG signaling cascade, suggesting that this pathway is a therapeutic target to reduce inflammatory tissue destruction in tuberculosis.
On impulse response modeling for underwater wireless optical MIMO links

In this paper, we consider the impulse response for underwater wireless optical communication (UWOC) links with multiple-input multiple-output (MIMO) configuration. The widely used Monte Carlo approach is employed to obtain the impulse response of 2-by-2 UWOC MIMO links for turbid water environment. We then present a weighted double Gamma functions (WDGF) model to represent the simulated impulse response. Numerical results suggest that the proposed WDGF model fits well with the impulse response of UWOC MIMO links in turbid seawater such as coastal and harbor water.
Awareness of Direct-to-Consumer Genetic Tests and Use of Genetic Tests Among Puerto Rican Adults, 2009

Introduction Genetic testing remains low among racial/ethnic minority populations in the United States. We aimed to determine the prevalence and correlates of awareness of direct-to-consumer (DTC) genetic tests and the prevalence of genetic test use in a population-based sample of adults in Puerto Rico. Methods We analyzed data from adults aged 18 years or older who completed information on genetic test awareness (n = 611; 96% of study population) from the Health Information National Trends Survey conducted in Puerto Rico in 2009. Odds ratios with 95% confidence intervals were estimated by using logistic regression models to identify factors associated with awareness of DTC genetic tests. Results The majority of respondents (56%) were aware of direct-to-consumer genetic tests, and approximately 4% had ever undergone any genetic test. Respondents who had never been married were less likely to be aware of DTC tests, as were current smokers. Respondents who ever sought cancer information were more likely to be aware of these tests. Conclusion We provide the first published data on the awareness of DTC genetic tests and on use of genetic testing in Puerto Rico. Forty-four percent of our sample of Puerto Rican adults were unaware of direct-to-consumer genetic tests. Given the lack of clear benefits of DTC genetic tests to the general population, educational interventions should be developed to increase awareness and specific knowledge regarding the appropriate use of DTC genetic tests among people who are already aware of their existence.
Clustering of Peptide-Loaded MHC Class I Molecules for Endoplasmic Reticulum Export Imaged by Fluorescence Resonance Energy Transfer1

Fluorescence resonance energy transfer between cyan fluorescent protein- and yellow fluorescent protein-tagged MHC class I molecules reports on their spatial organization during assembly and export from the endoplasmic reticulum (ER). A fraction of MHC class I molecules is clustered in the ER at steady state. Contrary to expectations from biochemical models, this fraction is not bound to the TAP. Instead, it appears that MHC class I molecules cluster after peptide loading. This clustering points toward a novel step involved in the selective export of peptide-loaded MHC class I molecules from the ER. Consistent with this model, we detected clusters of wild-type HLA-A2 molecules and of mutant A2-T134K molecules that cannot bind TAP, but HLA-A2 did not detectably cluster with A2-T134K at steady state. Lactacystin treatment disrupted the HLA-A2 clusters, but had no effect on the A2-T134K clusters. However, when cells were fed peptides with high affinity for HLA-A2, mixed clusters containing both HLA-A2 and A2-T134K were detected.
Vehicular sensor networks Authentication new approach

In this paper, we introduce a novel Physical layer Assisted message Authentication (PAA) under public key infrastructure (PKI) in vehicular communication networks. The novel authentication scheme takes advantage of temporal and spatial uniqueness in physical layer channel responses for each transmission pair, in which a trust between two vehicles can be maintained by comparing the current estimated channel response and the previous estimated channel response. We will show that the proposed message authentication scheme can achieve extremely high efficiency and minimal authentication delay without compromising the security requirements, which is further verified through both analysis and simulation.
Bearing Localized Fault Detection Based on Hilbert-Huang Transformation

The Hilbert-Huang transform and its marginal spectrum are applied to bearing fault diagnosis of ball bearing. The principle of Empirical mode decomposition (EMD), Hilbert-Huang transformation (HHT) and marginal spectrum is introduced. Firstly, the vibration signals of bearing fault are separated into several intrinsic mode functions (IMFs) using EMD method. Secondly, the marginal spectrum of each IMF is calculated. In the end, according to the marginal spectrum, the localized fault in a ball bearing can be detected and faults patterns can be identified. The experimental results show that the proposed method can provide not only an increase in the spectral resolution but also reliability for the faults diagnosis of ball bearing.
Patient‐reported Outcomes in Cancer: A Review of Recent Research and Policy Initiatives

There is growing recognition that patient‐reported outcome (PRO) measures—encompassing, for example, health‐related quality of life—can complement traditional biomedical outcome measures (eg, survival, disease‐free survival) in conveying important information for cancer care decision making. This paper provides an integrated review and interpretation of how PROs have been defined, measured, and used in a range of recent cancer research and policy initiatives. We focus, in turn, on the role of PRO measurement in the evaluation and approval of cancer therapies, the assessment of cancer care in the community, patient‐provider decision making in clinical oncology practice, and population surveillance of cancer patients and survivors. The paper concludes with a discussion of future challenges and opportunities in PRO measure development and application, given the advancing state of the science in cancer outcomes measurement and the evolving needs of cancer decision makers at all levels.
Adaptive predictive control of a high purity distillation column using irregularly sampled multi-rate data

This work aims at the development of multi-rate adaptive model predictive control (MR-AMPC) based on the fast rate model, which is identified from irregularly sampled multi-rate data. The model is assumed to have output error structure and is parameterized using generalized orthonormal basis filters. The identified model is used to generate inter-sample estimates of the irregularly sampled outputs and for performing future trajectory predictions in the proposed MRMPC formulation. The effectiveness of the proposed adaptive multi-rate control scheme is demonstrated by conducting simulation studies on a benchmark binary distillation column system[1]. The results from the simulation reveals that the proposed adaptive multi-rate model predictive control successfully manages transition of the distillation column from moderate purity region to the high purity region where the system exhibits highly nonlinear dynamics.
An Efficient Polarity Detection Technique for Thermoelectric Harvester in L-based Converters

This paper presents a new method for detecting and reversing the polarity of a low-voltage thermoelectric generator (TEG) in inductor-based converters. The proposed technique makes use of the inductor response to a voltage change due to the flip in the TEG polarity. The inductor voltage provides two distinguishable states which correspond to the normal and the reversed TEG polarity. A switch matrix circuit is then used to correct the polarity by physically reversing the TEG connection. The detection circuit along with the switch matrix provide a positive input voltage from the TEG to the inductor-based converter. The proposed technique is an efficient polarity detection with all-digital implementation, fully integrated, small area and power overhead. The prototype chip is fabricated in 65-nm CMOS and occupies an area of 0.09 mm2. Measurement results confirm a maximum efficiency of 70% at 50 mV TEG voltage and $40~\mu \text {A}$ output current. The proposed technique is part of an autonomous thermal energy harvesting system that detects and corrects the TEG polarity.
FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae

The heterotrophic marine bacterium Dinoroseobacter shibae utilizes aerobic respiration and anaerobic denitrification supplemented with aerobic anoxygenic photosynthesis for energy generation. The aerobic to anaerobic transition is controlled by four Fnr/Crp family regulators in a unique cascade-type regulatory network. FnrL is utilizing an oxygen-sensitive Fe-S cluster for oxygen sensing. Active FnrL is inducing most operons encoding the denitrification machinery and the corresponding heme biosynthesis. Activation of gene expression of the high oxygen affinity cbb3-type and repression of the low affinity aa3-type cytochrome c oxidase is mediated by FnrL. Five regulator genes including dnrE and dnrF are directly controlled by FnrL. Multiple genes of the universal stress protein (USP) and cold shock response are further FnrL targets. DnrD, most likely sensing NO via a heme cofactor, co-induces genes of denitrification, heme biosynthesis, and the regulator genes dnrE and dnrF. DnrE is controlling genes for a putative Na+/H+ antiporter, indicating a potential role of a Na+ gradient under anaerobic conditions. The formation of the electron donating primary dehydrogenases is coordinated by FnrL and DnrE. Many plasmid encoded genes were DnrE regulated. DnrF is controlling directly two regulator genes including the Fe-S cluster biosynthesis regulator iscR, genes of the electron transport chain and the glutathione metabolism. The genes for nitrate reductase and CO dehydrogenase are repressed by DnrD and DnrF. Both regulators in concert with FnrL are inducing the photosynthesis genes. One of the major denitrification operon control regions, the intergenic region between nirS and nosR2, contains one Fnr/Dnr binding site. Using regulator gene mutant strains, lacZ-reporter gene fusions in combination with promoter mutagenesis, the function of the single Fnr/Dnr binding site for FnrL-, DnrD-, and partly DnrF-dependent nirS and nosR2 transcriptional activation was shown. Overall, the unique regulatory network of the marine bacterium D. shibae for the transition from aerobic to anaerobic growth composed of four Crp/Fnr family regulators was elucidated.
Splicing of the Meiosis-Specific HOP2Transcript Utilizes a Unique 5′ Splice Site

ABSTRACT The Saccharomyces cerevisiae HOP2 gene is required to prevent formation of synaptonemal complex between nonhomologous chromosomes during meiosis. The HOP2 gene is expressed specifically in meiotic cells, with the transcript reaching maximum abundance early in meiotic prophase. The HOP2 coding region is interrupted by an intron located near the 5′ end of the gene. This intron contains a nonconsensus 5′ splice site (GUUAAGU) that differs from the consensus 5′ splice signal (GUAPyGU) by the insertion of a nucleotide and by a single nucleotide substitution. Bases flanking the HOP2 5′ splice site have the potential to pair with sequences in U1 small nuclear RNA, and mutations disrupting this pairing reduce splicing efficiency. HOP2pre-mRNA is spliced efficiently in the absence of the Mer1 and Nam8 proteins, which are required for splicing the transcripts of two other meiosis-specific genes.
Analysis of interregional industry linkage and economic distance in China: evidence from the mining industry

ABSTRACT The mining industry is an important sector of the national economy, which provides essential support for energy and other resources for economic development. Industrial linkage and economic distance are two different concepts in measuring the correlationship of different industries, in this article, we apply the model that combines both of them to analyse the industries significantly influence the mining industry. We find that electricity and heating industry, and the mining industry itself from forward linkages have greatly influenced the mining industry, and the industries from backward linkages affect mining industry are changing with industrial economic transformation. We also find resources can flow across several regions only after 2007, which means the role of geographical factors limiting long-range transportation of resources is weakening after 2007. And we explain how resources flow among various regions during 1997 ~ 2007. Based on the findings above, policy implications from the empirical results obtained are discussed.
Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci

Replicative senescence is the state of irreversible proliferative arrest that occurs as a concomitant of progressive telomere shortening. By using cDNA microarrays and the gabriel system of computer programs to apply domain-specific and procedural knowledge for data analysis, we investigated global changes in gene transcription occurring during replicative senescence in human fibroblasts and mammary epithelial cells (HMECs). Here we report the identification of transcriptional “fingerprints” unique to senescence, the finding that gene expression perturbations during senescence differ greatly in fibroblasts and HMECs, and the discovery that despite the disparate nature of the chromosomal loci affected by senescence in fibroblasts and HMECs, the up-regulated loci in both types of cells show physical clustering. This clustering, which contrasts with the random distribution of genes down-regulated during senescence or up-regulated during reversible proliferative arrest (i.e., quiescence), supports the view that replicative senescence is associated with alteration of chromatin structure.
A fully automatic redeye detection and correction algorithm

A fully automatic redeye detection and correction algorithm was developed at Eastman Kodak Company Research Laboratories. The algorithm is highly sophisticated so that it is able to distinguish most redeye pairs from scene content. It is also highly optimized for execution speed and memory usage enabling it to be included in a variety of products. Detected redeyes are corrected so that the red color is removed, but the eye maintains a natural look.
European voters in the face of crisis: the prominence of unemployment

From a political perspective, an economic crisis is an external shock which may deeply affect the functioning of a political system. Covering the European Parliament elections from 1999 to 2014, this article analyses how and to what extent the 2008 economic crisis affected the electoral patterns in EU member states. The analysis focusses on the electoral performance of both government parties and Eurosceptic parties, before and after the outbreak of the crisis. Resorting to the economic voting theory, it addresses two questions: first, if and why electoral losses of governing parties are greater during the crisis than before; and, second, if and why Eurosceptic parties have become more prominent after the onset of the crisis. Change of unemployment rate is shown as being the most important factor explaining these trends.
C-terminal Sequences Direct Cyclin D1-CRM1 Binding*

GSK-3β-dependent phosphorylation of cyclin D1 at a conserved C-terminal residue, Thr-286, promotes CRM1-dependent cyclin D1 nuclear export. Herein, we have identified a short stretch of residues adjacent to Thr-286 that mediates CRM1 association and thus cyclin D1 nuclear export. We found that disruption of this hydrophobic patch, stretching from amino acids 290 to 295 within cyclin D1, results in constitutively nuclear cyclin D1-CDK4 complexes with an increased propensity to potentiate transformation of murine fibroblasts. Our data support a model wherein deregulation of cyclin D1 nuclear export might contribute to human neoplastic growth.
Pseudomigraine With Prolonged Aphasia in a Child With Cranial Irradiation for Medulloblastoma

We report a 12-year-old child with episodes of migraine-like headaches with visual and motor auras a year after the surgical resection and radiation therapy for medulloblastoma. The patient presented with an episode of headache, prolonged aphasia, right hemiparesis, status epilepticus, and salt wasting. There was no evidence of a structural lesion. The neurologic deficits resolved over a period of 6 weeks. Because of the progressive deterioration in neurologic deficits, the patient underwent an extensive battery of laboratory tests and multiple neuroimages, all of which were normal. The unusually prolonged neurologic deficit in this patient without demonstrable structural lesions and his eventual complete recovery were most likely caused by ischemia in the left hemisphere secondary to vasospasm. This presentation mimics migraine headache. Evidence suggesting that this represents a long-term complication of treatment of children with central nervous system neoplasia is presented. (J Child Neurol 2002;17:134-138).
AEBP1 gene variants in infants with gastroschisis.

BACKGROUND The AEBP1 (adipocyte enhancer binding protein) gene has two isoforms: AEBP1, the shorter of the two isoforms, and Aclp (aortic carboxypeptidase-like protein). Aclp(-/-) mice demonstrate a ventral wall defect that is similar to gastroschisis in humans. Aclp is a potential candidate gene because it is expressed in numerous tissues during early development in mice; it associates with the extracellular matrix; and is essential for abdominal wall development and wound healing. In contrast, AEBP1 encodes an intracellular protein involved in proinflammatory responses, and may play a critical role in apoptosis and cell survival. Gastroschisis is a severe abdominal wall defect more common in young women and recently associated with a genitourinary infection early in pregnancy. METHODS We screened AEBP1 in 40 cases of gastroschisis and compared identified variants in a control population. RESULTS We identified several novel variants in AEBP1, including synonymous and nonsynonymous single nucleotide substitutions and intronic indels. However, the frequency of these variants was not significantly different from that of the control group, and the associated amino acid changes were predicted to be benign by two prediction software programs. CONCLUSIONS Gastroschisis remains an intriguing defect that, for an unknown reason, occurs more commonly in young women and after a genitourinary infection. Although we found many alterations in AEBP1 among the gastroschisis cases, they were predicted to be benign. However, this gene requires further understanding of its interaction with other genes involved in the immune response pathway.
On-line new event detection using time window strategy

New Event Detection is the task of automatically detecting novel events from a temporally-ordered stream of news story documents. Traditionally, on-line new event detection system determines whether the incoming document contains a new event based on the history of all processed documents. With the improvement of processed documents, the efficiency of on-line new event detection will decrease. In this paper, we apply a time window strategy to new event detection. A group of new incoming documents in the time window are firstly clustered to obtain candidate topics. Next, these candidate topics are compared with the previously identified topics to determine whether a new topic is detected. The first story of the new detected topic, in temporal order, is regarded as a new event. By analyzing the news story documents within the time window in group, the new event detection efficiency is improved. Furthermore, the evaluations show that the time window processing strategy is helpful to improve the accuracy of new event detection.
Dual impacts of climate change: forest migration and turnover through life history

Tree species are predicted to track future climate by shifting their geographic distributions, but climate‐mediated migrations are not apparent in a recent continental‐scale analysis. To better understand the mechanisms of a possible migration lag, we analyzed relative recruitment patterns by comparing juvenile and adult tree abundances in climate space. One would expect relative recruitment to be higher in cold and dry climates as a result of tree migration with juveniles located further poleward than adults. Alternatively, relative recruitment could be higher in warm and wet climates as a result of higher tree population turnover with increased temperature and precipitation. Using the USDA Forest Service's Forest Inventory and Analysis data at regional scales, we jointly modeled juvenile and adult abundance distributions for 65 tree species in climate space of the eastern United States. We directly compared the optimal climate conditions for juveniles and adults, identified the climates where each species has high relative recruitment, and synthesized relative recruitment patterns across species. Results suggest that for 77% and 83% of the tree species, juveniles have higher optimal temperature and optimal precipitation, respectively, than adults. Across species, the relative recruitment pattern is dominated by relatively more abundant juveniles than adults in warm and wet climates. These different abundance‐climate responses through life history are consistent with faster population turnover and inconsistent with the geographic trend of large‐scale tree migration. Taken together, this juvenile–adult analysis suggests that tree species might respond to climate change by having faster turnover as dynamics accelerate with longer growing seasons and higher temperatures, before there is evidence of poleward migration at biogeographic scales.