Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic architecture of the adjacent airway field cancerization in non-small cell lung cancer.

BACKGROUND Earlier work identified specific tumor-promoting abnormalities that are shared between lung cancers and adjacent normal bronchial epithelia. We sought to characterize the yet unknown global molecular and adjacent airway field cancerization (FC) in early-stage non-small cell lung cancer (NSCLC). METHODS Whole-transcriptome expression profiling of resected early-stage (I-IIIA) NSCLC specimens (n = 20) with matched tumors, multiple cytologically controlled normal airways with varying distances from tumors, and uninvolved normal lung tissues (n = 194 samples) was performed using the Affymetrix Human Gene 1.0 ST platform. Mixed-effects models were used to identify differentially expressed genes among groups. Ordinal regression analysis was performed to characterize site-dependent airway expression profiles. All statistical tests were two-sided, except where noted. RESULTS We identified differentially expressed gene features (n = 1661) between NSCLCs and airways compared with normal lung tissues, a subset of which (n = 299), after gene set enrichment analysis, statistically significantly (P < .001) distinguished large airways in lung cancer patients from airways in cancer-free smokers. In addition, we identified genes (n = 422) statistically significantly and progressively differentially expressed in airways by distance from tumors that were found to be congruently modulated between NSCLCs and normal lung tissues. Furthermore, LAPTM4B, with statistically significantly increased expression (P < .05) in airways with shorter distance from tumors, was upregulated in human immortalized cells compared with normal bronchial epithelial cells (P < .001) and promoted anchorage-dependent and -independent lung cancer cell growth. CONCLUSIONS The adjacent airway FC comprises both site-independent profiles as well as gradient and localized airway expression patterns. Profiling of the airway FC may provide new insights into NSCLC oncogenesis and molecular tools for detection of the disease.
The Politics of Chinese Media: Consensus and Contestation

This book offers an analytical account of the consensus and contestations of the politics of Chinese media at both institutional and discursive levels. It considers the formal politics of how the Chinese state manages political communication internally and externally in the post-socialist era, and examines the politics of news media, focusing particularly on how journalists navigate the competing demands of the state, the capital and the urban middle class readership. The book also addresses the politics of entertainment media, in terms of how power operates upon and within media culture, and the politics of digital networks, highlighting how the Internet has become the battlefield of ideological contestation while also shaping how political negotiations are conducted. Bearing in mind the contemporary relevance of China’s socialist revolution, this text challenges both the liberal universalist view that presupposes ‘the end of history’ and various versions of China exceptionalism, which downplay the impact of China’s integration into global capitalism.
Multivariate Analysis of Hemicelluloses in Bleached Kraft Pulp Using Infrared Spectroscopy

The hemicellulose composition of a pulp significantly affects its chemical and physical properties and thus represents an important process control variable. However, complicated steps of sample preparation make standard methods for the carbohydrate analysis of pulp samples, such as high performance liquid chromatography (HPLC), expensive and time-consuming. In contrast, pulp analysis by attenuated total internal reflection Fourier transform infrared spectroscopy (ATR FT-IR) requires little sample preparation. Here we show that ATR FT-IR with discrete wavelet transform (DWT) and standard normal variate (SNV) spectral preprocessing offers a convenient means for the qualitative and quantitative analysis of hemicelluloses in bleached kraft pulp and alkaline treated kraft pulp. The pulp samples investigated include bleached softwood kraft pulps, bleached hardwood kraft pulps, and their mixtures, as obtained from Canadian industry mills or blended in a lab, and bleached kraft pulp samples treated with 0–6% NaOH solutions. In the principal component analysis (PCA) of these spectra, we find the potential both to differentiate all pulps on the basis of hemicellulose compositions and to distinguish bleached hardwood pulps by species. Partial least squares (PLS) multivariate analysis gives a 0.442 wt% root mean square errors of prediction (RMSEP) for the prediction of xylan content and 0.233 wt% RMSEP for the prediction of mannan content. These data all support the idea that ATR FT-IR has a great potential to rapidly and accurately predict the content of xylan and mannan for bleached kraft pulps (softwood, hardwood, and their mixtures) in industry. However, the prediction of xylan and mannan concentrations presented a difficulty for pulp samples with modified cellulose crystalline structure.
Ethnoracial Attitudes and Identity-Salient Experiences Among Indigenous Mexican Adolescents and Emerging Adults

This interdisciplinary study drew on Critical Latinx Indigeneities and Nigrescence Theory to conduct a mixed-method analysis of the ethnoracial attitudes and identity-salient experiences of Indigenous Oaxaqueño adolescents and emerging adults living in the United States. Results revealed that compared to emerging adults, adolescents endorsed higher self-hatred and lower multiculturalist inclusive attitudes. The ethnoracial attitudes of adolescents’, but not of emerging adults’, were correlated with their reported discrimination from mestizo Mexican peers. Narrative analysis revealed four types of experiences that defined what it means to be Oaxaqueño: cultural practices, ethnoracial discrimination, connection, and a disconnect with an Indigenous identity. Findings highlight the need for existing ethnoracial identity theories and scales to consider the multiracial and colonial structure within which Latinx youth develop their identities.
DAP-5, a novel homolog of eukaryotic translation initiation factor 4G isolated as a putative modulator of gamma interferon-induced programmed cell death

A functional approach to gene cloning was applied to HeLa cells in an attempt to isolate cDNA fragments which convey resistance to gamma interferon (IFN-gamma)-induced programmed cell death. One of the rescued cDNAs, described in this work, was a fragment of a novel gene, named DAP-5. Analysis of a DAP-5 full-length cDNA clone revealed that it codes for a 97-kDa protein that is highly homologous to eukaryotic translation initiation factor 4G (eIF4G, also known as p220). According to its deduced amino acid sequence, this novel protein lacks the N-terminal region of eIF4G responsible for association with the cap binding protein eIF4E. The N-terminal part of DAP-5 has 39% identity and 63% similarity to the central region of mammalian p220. Its C-terminal part is less homologous to the corresponding region of p220, suggesting that it may possess unique functional properties. The rescued DAP-5 cDNA fragment which conveyed resistance to IFN-gamma-induced cell death was expressed from the vector in the sense orientation. Intriguingly, it comprised part of the coding region which corresponds to the less conserved C-terminal part of DAP-5 and directed the synthesis of a 28-kDa miniprotein. The miniprotein exerted a dual effect on HeLa cells. Low levels of expression protected the cells from IFN-gamma-induced programmed cell death, while high levels of expression were not compatible with continuous cell growth. The relevance of DAP-5 protein to possible changes in a cell's translational machinery during programmed cell death and growth arrest is discussed.
Exploring the correlation between the folding rates of proteins and the entanglement of their native states

The folding of a protein towards its native state is a rather complicated process. However, there is empirical evidence that the folding time correlates with the contact order, a simple measure of the spatial organization of the native state of the protein. Contact order is related to the average length of the main chain loops formed by amino acids that are in contact. Here we argue that folding kinetics can also be influenced by the entanglement that loops may undergo within the overall three-dimensional protein structure. In order to explore such a possibility, we introduce a novel descriptor, which we call ‘maximum intrachain contact entanglement’. Specifically, we measure the maximum Gaussian entanglement between any looped portion of a protein and any other non-overlapping subchain of the same protein, which is easily computed by discretized line integrals on the coordinates of the Cα atoms. By analyzing experimental data sets of two-state and multi-state folders, we show that the new index is also a good predictor of the folding rate. Moreover, being only partially correlated with previous methods, it can be integrated with them to yield more accurate predictions.
Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning

We report the presence of long stretches of tandem repeats in the genome of the halophilic Archaea Haloferax mediterranei and Haloferax volcanii A 30 bp sequence with dyad symmetry (including 5 bp inverted repeats) was repeated in tandem, interspersed with 33–39 bp unique sequences. This structure extends for long stretches — 1.4kb at one location in H. mediterranei chromosome and about 3kb in the H. volcanii chromosome. The tandem repeats (designated TREPs) show a similar distribution in both organisms, appearing once or twice in the H. volcanii and H. mediterranei chromosomes, and once in the largest, probably essential megaplasmid of each organism but not in the smaller replicons. Sequencing of the structures in both H. volcanii replicons revealed an extremely high sequence conservation in both replicons within the species, as well as in the different organisms. Homologous sequences have also been found in other more distantly related halophilic members of the Archaea. Transformation of H. volcanii with a recombinant plasmid containing a 1.1 kb fragment of the TREPs produced significant alterations in the host cells, particularly in terms of cell viability. The introduction of extra copies of TREPs within the vector significantly alters the distribution of the genome among the daughter cells, as observed by DAPI staining. Although the precise biological role cannot be completely ascertained, all the data conform with the tandem repeats being involved in replicon partitioning in halobacteria.
Individual and Mixture Toxicity of Three Pesticides; Atrazine, Chlorpyrifos, and Chlorothalonil to the Marine Phytoplankton Species Dunaliella tertiolecta

This study analyzed the toxicity of three pesticides (the herbicide atrazine, the insecticide chlorpyrifos and the fungicide chlorothalonil) individually, and in two mixtures (atrazine and chlorpyrifos; atrazine and chlorothalonil) to the marine phytoplankton species Dunaliella tertiolecta (Chlorophyta). A standard 96 h static algal bioassay was used to determine pesticide effects on the population growth rate of D. tertiolecta. Mixture toxicity was assessed using the additive index approach. Atrazine and chlorothalonil concentrations ≥ 25 µg/L and 33.3 µg/L, respectively, caused significant decreases in D. tertiolecta population growth rate. At much higher concentrations (≥ 400 µg/L) chlorpyrifos also elicited a significant effect on D. tertiolecta population growth rate, but toxicity would not be expected at typical environmental concentrations. The population growth rate EC50 values determined for D. tertiolecta were 64 µg/L for chlorothalonil, 69 µg/L for atrazine, and 769 µg/L for chlorpyrifos. Atrazine and chlorpyrifos in mixture displayed additive toxicity, whereas atrazine and chlorothalonil in mixture had a synergistic effect. The toxicity of atrazine and chlorothalonil combined was approximately 2 times greater than that of the individual chemicals. Therefore, decreases in phytoplankton populations resulting from pesticide exposure could occur at lower than expected concentrations in aquatic systems where atrazine and chlorothalonil are present in mixture. Detrimental effects on phytoplankton population growth rate could impact nutrient cycling rates and food availability to higher trophic levels. Characterizing the toxicity of chemical mixtures likely to be encountered in the environment may benefit the pesticide registration and regulation process.
TGF‐β1 serum concentration as a complementary diagnostic biomarker of lung cancer: establishment of a cut‐point value

Lung cancer is a malignant disease with increasing mortality rates. Cytokines play a role in normal cell growth regulation and differentiation and are also implicated in malignant disease. Among these cytokines, Transforming Growth Factor β type 1 (TGF‐β1) acts as a tumor promoter in malignant cells. Several clinical studies have found high levels of TGF‐β1 in various cancer types. The aim of this study was to establish a TGF‐β1 cut‐off point as a complementary diagnostic tool in lung cancer detection. Therefore, 72 clinically well‐characterized individuals were studied, 41 lung cancer patients and 31 healthy subjects. Serum TGF‐β1 concentration was measured by an enzyme‐linked immunosorbent assay (ELISA). We compared statistically the serum TGF‐β1 concentration between both groups with analysis of variance, linear regression and receiver operating curve analysis. We observed that lung cancer patients produced higher TGF‐β1 levels than healthy individuals (37,225±9,436 vs. 28,416±9,324 pg/ml, P<0.001). The cut‐point diagnostic value was 30,500 pg/ml with 80.5% sensitivity, 64.5% specificity and odds ratio: 7.5, 95% CI: 2.6–21.8. Conclusions: We found significantly higher TGF‐β1 levels in lung cancer patients than in healthy individuals. We propose the measurement of serum TGF‐β1 levels as a complementary diagnostic test in lung cancer detection. J. Clin. Lab. Anal. 25:238–243, 2011. © 2011 Wiley‐Liss, Inc.
The Influence of Different Plasticizers and Polymers on the Mechanical and Thermal Properties, Porosity and Drug Permeability of Free Shellac Films

ABSTRACT The effect of triethyl citrate (TEC) and different molecular weights and concentrations of polyethylene glycol (PEG), in addition to the effect of different water-soluble polymers and dispersions at different levels, hydroxypropyl methylcellulose (HPMC), methylcellulose (MC), carbomer 940, polyvinyl alcohol (PVA), ethyl cellulose (EC), on the mechanical and thermal properties, drug permeability, and porosity of free shellac films were investigated. Shellac films were cast from aqueous solutions, and their mechanical properties were studied by tensile test. Thermal analyses were performed using differential scanning calorimetry (DSC). The results showed that the addition of plasticizer caused a decrease in both elastic modulus and glass transition temperature (Tg) and an increase in elongation at break of free shellac films. This effect was related to the concentrations of plasticizers. Different molecular weights of PEGs have different plasticization mechanisms. Moreover, the incorporation of different amounts of HPMC, MC, or carbomer in free shellac films caused an increase in the flexibility, decrease in Tg, and a marked increase in drug permeability of free shellac films, whereas the addition of PVA caused a decrease in flexibility and drug permeability and an increase in Tg. Addition of EC resulted in a slight decrease of the elasticity and a small decrease in drug permeability. However it does not show a considerable effect on the Tg. In addition, it was found that the drug permeability is directly related to the mechanical properties and Tg of shellac films.
Outcome of infants operated on for congenital pulmonary malformations

: Patients operated on for congenital pulmonary malformations (CPM) have excellent survival rates, but little is known about long‐term morbidity. Our aim is to report the sequelae in patients operated on for CPM in infancy and to define factors that may influence their outcome. Methods: All patients operated on for major congenital anomalies are followed in a dedicated outpatient program and evaluated at 6, 24, and 48 months of life (corrected for gestational age) and at school age at 4, 6, 8, and 12 years of life. The data are prospectively collected. Patients operated on for CPM and enrolled in the follow‐up clinic between January 2004 and December 2010 are compared with a control group of term infants operated on for inguinal hernia, without other major congenital or acquired abnormalities. The two groups were compared for auxological, respiratory, and orthopedic outcome. Results: In the study period, 76 consecutive patients with CPM attended our dedicated follow‐up clinic. Eight non‐operated patients were excluded from the study. Age at follow‐up was 82.0 (56.1–103.7) months in CPM patients and 83.5 (75.2–90.4) months in controls (P = 0.79). Fifty‐three patients with CPM (78%) had one or more clinical or radiological abnormality versus six (16%) control patients (OR [95%CI] 16.5 [5.8–47.2]; P < 0.0001). Conclusions: Over 50% of patients with CPM present long‐term sequelae, regardless type of malformation. Therefore, long‐term follow‐up of patients operated on for CPM is recommended. Further studies are needed to define if, in asymptomatic patients, surgery may modify the natural history of CPM. Pediatr Pulmonol. 2016;51:1367–1372. © 2016 Wiley Periodicals, Inc.
Role of CD4+ and CD8+ T Cells in Allorecognition: Lessons from Corneal Transplantation1

Corneal transplantation represents an interesting model to investigate the contribution of direct vs indirect Ag recognition pathways to the alloresponse. Corneal allografts are naturally devoid of MHC class II+ APCs. In addition, minor Ag-mismatched corneal grafts are more readily rejected than their MHC-mismatched counterparts. Accordingly, it has been hypothesized that these transplants do not trigger direct T cell alloresponse, but that donor Ags are presented by host APCs, i.e., in an indirect fashion. Here, we have determined the Ag specificity, frequency, and phenotype of T cells activated through direct and indirect pathways in BALB/c mice transplanted orthotopically with fully allogeneic C57BL/6 corneas. In this combination, only 60% of the corneas are rejected, while the remainder enjoy indefinite graft survival. In rejecting mice the T cell response was mediated by two T cell subsets: 1) CD4+ T cells that recognize alloantigens exclusively through indirect pathway and secrete IL-2, and 2) IFN-γ-producing CD8+ T cells recognizing donor MHC in a direct fashion. Surprisingly, CD8+ T cells activated directly were not required for graft rejection. In nonrejecting mice, no T cell responses were detected. Strikingly, peripheral sensitization to allogeneic MHC molecules in these mice induced acute rejection of corneal grafts. We conclude that only CD4+ T cells activated via indirect allorecognition have the ability to reject allogeneic corneal grafts. Although alloreactive CD8+ T cells are activated via the direct pathway, they are not fully competent and cannot contribute to the rejection unless they receive an additional signal provided by professional APCs in the periphery.
Scapular Muscle Activity in Overhead and Nonoverhead Athletes During Closed Chain Exercises

Objective:To compare scapular muscle activity in healthy overhead and nonoverhead athletes. Design:One between (group) and 1 within (exercise) repeated measures. Setting:Controlled laboratory environment. Participants:Fifteen overhead sport athletes (10 women and 5 men) and 15 nonoverhead sport athletes (10 women and 5 men). Interventions:Subjects completed 5 individual trials of a Cuff Link, standard push-up, and supine pull-up while surface electromyography (EMG) recorded muscle activity of 4 scapular muscles on the throwing dominant side. Mean EMG data were normalized to a maximum voluntary isometric contraction. Main Outcome Measures:Normalized mean EMG. Results:The upper trapezius was significantly more active (F2,56 = 70.118; P < 0.001) during supine pull-up (61.57 ± 29.67%) than during push-up (27.89 ± 16.21%) and Cuff Link (5.50 ± 2.94%). The middle trapezius was significantly more active (F2,56 = 134.192; P < 0.001) during supine pull-up (62.89 ± 24.17%) than during push-up (21.12 ± 13.10%) and Cuff Link (6.59 ± 4.81%). The lower trapezius was significantly more active (F2,56 = 41.326; P < 0.001) during supine pull-up (60.47 ± 34.80%) than during push-up (34.80 ± 30.81%) and Cuff Link (9.67 ± 4.34%). For upper trapezius, middle trapezius, and lower trapezius, the levels of activation during push-up were significantly greater compared with those during Cuff Link. The serratus anterior was significantly more active (F2,56 = 25.652; P < 0.001) during push-up (49.97 ± 18.86%) and Cuff Link (43.81 ± 19.70%) than during supine pull-up (25.52 ± 19.80%). There were no significant influences of group on muscle activation. Conclusions:Overhead and nonoverhead athletes elicited similar levels of muscle activation. Differences in muscle activation existed within the 3 exercises. Clinicians should consider the muscle of interest when prescribing one of these exercises.
Are occupational factors important determinants of socioeconomic inequalities in musculoskeletal pain?

OBJECTIVES The aim of this study was to quantify socioeconomic inequalities in low-back pain, neck-shoulder pain, and arm pain in the general working population in Oslo and to examine the impact of job characteristics on these inequalities. METHODS All economically active 30-, 40-, and 45-year-old persons who attended the Oslo health study in 2000-2001 and answered questions on physical job demands, job autonomy, and musculoskeletal pain were included (N=7293). Occupational class was used as an indicator of socioeconomic status. The lower occupational classes were compared with higher grade professionals, and prevalences, prevalence ratios, prevalence differences, and population attributable fractions were calculated. RESULTS There were marked, stepwise socioeconomic gradients for musculoskeletal pain, steeper for the men than for the women. The relative differences (prevalence ratios) were larger for low-back pain and arm pain than for neck-shoulder pain. The absolute differences (prevalence differences) were the largest for low-back pain. Physical job demands explained a substantial proportion of the absolute occupational class inequalities in low-back pain, while job autonomy was more important in explaining the inequalities in neck-shoulder pain and arm pain. The estimated population attributable fractions supported the impact of job characteristics at the working population level, especially for low-back pain. CONCLUSIONS In this cross-sectional study, physical job demands and job autonomy explained a substantial proportion of occupational class inequalities in self-reported musculoskeletal pain in the working population in Oslo. This finding indicates that the workplace may be an important arena for preventive efforts to reduce socioeconomic inequalities in musculoskeletal pain.