Miracle-dz/UniFAR-FTUs huggingface dataset:
Wnt and FGF mediated epithelial‐mesenchymal crosstalk during lung development

Background: The adaptation to terrestrial life required the development of an organ capable of efficient air‐blood gas exchange. To meet the metabolic load of cellular respiration, the mammalian respiratory system has evolved from a relatively simple structure, similar to the two‐tube amphibian lung, to a highly complex tree‐like system of branched epithelial airways connected to a vast network of gas exchanging units called alveoli. The development of such an elaborate organ in a relatively short time window is therefore an extraordinary feat and involves an intimate crosstalk between mesodermal and endodermal cell lineages. Results: This review describes the molecular processes governing lung development with an emphasis on the current knowledge on the role of Wnt and FGF signaling in lung epithelial differentiation. Conclusions: The Wnt and FGF signaling pathways are crucial for the dynamic and reciprocal communication between epithelium and mesenchyme during lung development. In addition, some of this developmental crosstalk is reemployed in the adult lung after injury to drive regeneration, and may, when aberrantly or chronically activated, result in chronic lung diseases. Novel insights into how the Wnt and FGF pathways interact and are integrated into a complex gene regulatory network will not only provide us with essential information about how the lung regenerates itself, but also enhance our understanding of the pathogenesis of chronic lung diseases, as well as improve the controlled differentiation of lung epithelium from pluripotent stem cells. Developmental Dynamics 244:342–366, 2015. © 2014 Wiley Periodicals, Inc.
Potential Implications of Missing Income Data in Population-Based Surveys: An Example from a Postpartum Survey in California

Objectives. Income data are often missing for substantial proportions of survey participants and these records are often dropped from analyses. To explore the implications of excluding records with missing income, we examined characteristics of survey participants with and without income information. Methods. Using statewide population-based postpartum survey data from the California Maternal and Infant Health Assessment, we compared the age, education, parity, marital status, timely prenatal care initiation, and neighborhood poverty characteristics of women with and without reported income data, overall, and by race/ethnicity/nativity. Results. Overall, compared with respondents who reported income, respondents with missing income information generally appeared younger, less educated, and of lower parity. They were more likely to be unmarried, to have received delayed or no prenatal care, and to reside in poor neighborhoods; and they generally appeared more similar to lower- than higher-income women. However, the patterns appeared to vary by racial/ethnic/nativity group. For example, among U.S.-born African American women, the characteristics of the missing-income group were generally similar to those of low-income women, while European American women with missing income information more closely resembled their moderate-income counterparts. Conclusions. Respondents with missing income information may not be a random subset of population-based survey participants and may differ on other relevant sociodemographic characteristics. Before deciding how to deal analytically with missing income information, researchers should examine relevant characteristics and consider how different approaches could affect study findings. Particularly for ethnically diverse populations, we recommend including a missing income category or employing multiple-imputation techniques rather than excluding those records.
The effect of malintent on visual attention

THE EFFECT OF MALINTENT ON VISUAL ATTENTION by David Brian Wallace Adviser: Dr. Maria Hartwig Malintent is a relatively unexplored phenomenon, despite the practical and theoretical interest in its detection. The four studies presented here, informed by the Guilty Knowledge Test and Guided Search model of visual attention, illustrate how eye tracking can (and cannot) be utilized to detect malicious intent. Malintent, induced in two different mock crime paradigms (murder; theft), boosted the frequency and duration of fixations that fell upon objects relevant to their task. The size of the malintent effect ranged from moderate (fixation duration) to large (fixation frequency). The increased visual attention given to task-relevant objects was not unique to malintent; benign intent individuals, given the same task to perform without the transgressive framing, showed similar gaze patterns when they were unaware of the eye-tracking equipment. When made aware that their gaze was being tracked, those with malintent successfully avoided looking at the task-relevant object, while those with benign intent looked at it more often. The large moderating effect of eye-tracking awareness on the malintent effect poses both a challenge and an opportunity to the successful detection of malintent.
Cognitive Structures and Processes in Cross-Cultural Management

Controversies about the psychological implications of culture pervade the crosscultural management literature. When management scholars presume that psychological topics are universal, they are berated for their ethnocentrism (Boyacigiller & Adler, 1991; Wilpert, 1995). However, attempts to link psychology with culture face the dual perils of attributing psychological qualities to societies or cultural qualities to individuals (Hofstede, 2001; Smith, 2004). Despite these perils, social and organizational psychologists have drawn from cognitive theory to connect culture and psychology in ways that are useful for crosscultural management research (Smith, Bond & Kagitcibasi, 2006). The present chapter begins by considering theories of motivation and personality, the psychological theories that build most directly on the perspective on values provided in Chapter 1. We then consider ways in which cognitive theory helps understanding of the link from person to culture by analyzing the proactive development of cultural mastery or expertise. In particular, we consider those research purposes for which a person’s society of origin may be a better indicator of cognitive characteristics than are the values that a person endorses on a questionnaire. Finally, we describe some core findings from cognitive psychology and suggest research agendas that link dimensional theories, recent cognitive theory, and the social structures of organizations. Throughout the chapter, we take the position that the treatment of motivation and personality dimensions in the field of cross cultural management is frequently dated and overly rationalistic. We propose that the field needs to draw from the major advances in psychology of the past three decades by placing
Dietary omega-3 fatty acids and fish consumption and risk of type 2 diabetes.

BACKGROUND Although dietary omega-3 (n-3) fatty acids may confer some cardiovascular benefits, it is unclear whether these nutrients may also unfavorably affect risk of type 2 diabetes (T2D). OBJECTIVE We evaluated whether dietary omega-3 fatty acids and fish consumption were associated with increased risk of T2D. DESIGN This was a prospective study of 36,328 women (mean age: 54.6 y) who participated in the Women's Health Study and who were followed from 1992 to 2008. Incident T2D was self-reported and validated primarily through the collection of supplementary information from participants. Information on omega-3 and fish intakes was obtained by using a validated food-frequency questionnaire. We used Cox proportional hazard models to estimate adjusted relative risks. RESULTS During an average follow-up of 12.4 y, 2370 women developed T2D. Marine but not plant-based omega-3 fatty acids were positively associated with incident T2D. From the lowest to highest quintiles of marine omega-3 intake, the multivariable-adjusted hazard ratios (95% CIs) for T2D were 1.0 (referent), 1.17 (1.03, 1.33), 1.20 (1.05, 1.38), 1.46 (1.28, 1.66), and 1.44 (1.25, 1.65), respectively (P for trend < 0.0001). A similar association was observed with fish intake, but additional adjustment for docosahexaenoic acid led to the elimination of the association. The relation between marine omega-3 fatty acids and T2D was observed in hypertensive and nonhypertensive subjects and in women who reported infrequent fish consumption. CONCLUSION Our data suggest an increased risk of T2D with the intake of long-chain omega-3 fatty acids, especially with higher intakes (≥ 0.20 g omega-3/d or ≥ 2 servings of fish/d). The Women's Health Study was registered at clinicaltrials.gov as NCT00000479.
c-Met confers protection against chronic liver tissue damage and fibrosis progression after bile duct ligation in mice.

BACKGROUND & AIMS The hepatocyte growth factor (HGF)/mesenchymal-epithelial transition factor (c-Met) system is an essential inducer of hepatocyte growth and proliferation. Although a fundamental role for the HGF receptor c-Met has been shown in acute liver regeneration, its cell-specific role in hepatocytes during chronic liver injury and fibrosis progression has not been determined. METHODS Hepatocyte-specific c-Met knockout mice (c-Met(Delta hepa)) using the Cre-loxP system were studied in a bile duct ligation (BDL) model. Microarray analyses were performed to define HGF/c-Met-dependent gene expression. RESULTS Two strategies for c-Met deletion in hepatocytes to generate hepatocyte-specific c-Met knockout mice were tested. Early deletion during embryonic development was lethal, whereas post-natal Cre expression was successful, leading to the generation of viable c-Met(Delta hepa) mice. BDL in these mice resulted in extensive necrosis and lower proliferation rates of hepatocytes. Gene array analysis of c-Met(Delta hepa) mice revealed a significant reduction of anti-apoptotic genes in c-Met-deleted hepatocytes. These findings could be tested functionally because c-Met(Delta hepa) mice showed a stronger apoptotic response after BDL and Jo-2 stimulation. The phenotype was associated with increased expression of proinflammatory cytokines (tumor necrosis factor-alpha and interleukin-6) and an enhanced recruitment of neutrophils. Activation of these mechanisms triggered a stronger profibrogenic response as evidenced by increased transforming growth factor-beta(1), alpha-smooth muscle actin, collagen-1alpha messenger RNA expression, and enhanced collagen-fiber staining in c-Met(Delta hepa) mice. CONCLUSIONS Our results show that deletion of c-Met in hepatocytes leads to more liver cell damage and fibrosis in a chronic cholestatic liver injury model because c-Met triggers survival signals important for hepatocyte recovery.
Low-volume polyethylene glycol and bisacodyl for bowel preparation prior to colonoscopy: a meta-analysis

Background Quality of bowel preparation prior to colonoscopy is essential. Studies have shown a reduced volume of polyethylene glycol (PEG) with bisacodyl may improve visualization and tolerability, but results have varied. Therefore, a meta-analysis was performed to analyze the efficacy of a low-volume PEG bowel preparation with bisacodyl for bowel preparation prior to colonoscopy. Methods Multiple databases were searched (June 2012). Only randomized controlled trials in peer-reviewed journals on adult subjects comparing low-volume PEG (2 L) with bisacodyl versus 4 L PEG were included. Meta-analysis for the efficacy of low-volume PEG with bisacodyl and 4 L PEG were analyzed by calculating pooled estimates of number of satisfactory, excellent, and poor bowel preparations as well as adverse patient events (abdominal pain, nausea, vomiting, bloating). Results Six studies (N=1,540) met the inclusion criteria. No statistically significant differences were noted between low-volume PEG (2 L) with bisacodyl and 4 liters PEG for number of satisfactory (OR 0.86; 95% CI: 0.45-1.63, P=0.64), excellent (OR 1.08; 95% CI: 0.78-1.50, P=0.63), or poor bowel preparations (OR 0.68; 95% CI: 0.35-1.34, P=0.27). A statistically significant decrease in nausea (OR 0.57; 95% CI: 0.36-0.89, P=0.01), vomiting (OR 0.57; 95% CI: 0.40-0.81, P<0.01), and bloating (OR 0.65; 95% CI: 0.49-0.87, P<0.01) was noted for the low-volume PEG with bisacodyl as compared to 4 L PEG. No statistically significant differences were noted between the two groups for abdominal pain (P=0.62). Conclusion Low-volume PEG (2 L) with bisacodyl demonstrates less nausea, vomiting, and bloating without adversely affecting the bowel preparation.
Flows Reduction Scheme Using Two MPLS Tags in Software-Defined Network

This paper proposes a scheme to reduce the number of flow entries permanently stored in an OpenFlow switch and the number of configuration messages from a controller in a software-defined network (SDN). In an SDN, a flow table in an OpenFlow switch is used to instruct packets. The flow table consists of flow entries decided by the controller. A flow request is sent from the OpenFlow switch to the controller if the incoming packet does not match any flow entry in the flow table. The controller’s central processing unit may be overloaded to handle user requests, since the user requests for different data types have been rapidly increasing. As a result, flow configuration in switches is delayed. Moreover, the control plane may be flooded by configuration messages of those requests. A scheme to permanently keep the flow entries in the switch can reduce the number of requests. However, a large number of permanent flow entries is required. Other switch features may be degraded, since there is not enough memory in the flow table to implement those features. In the proposed scheme, switches in the network are divided into multiple regions. In order to guide packets from sources to destinations, the flow table incorporating the concept of two multiprotocol label switching tags is re-designed. One tag directs a packet from a source switch to an edge switch in the destination region. The other tag directs the packet from that edge switch to another switch in the same region. A mathematical model for the proposed scheme is formulated as an integer linear programming to determine a set of switches in each region so that the total number of permanent flow entries in the network can be minimized. The performance of the proposed scheme is analyzed. Moreover, the proposed scheme is implemented and demonstrated via Japanese Science Information Network 5.
Cleavage Map and Proteolytic Processing of the Murine Norovirus Nonstructural Polyprotein in Infected Cells

ABSTRACT Murine norovirus (MNV) is presently the only member of the genus Norovirus in the Caliciviridae that can be propagated in cell culture. The goal of this study was to elucidate the proteolytic processing strategy of MNV during an authentic replication cycle in cells. A proteolytic cleavage map of the ORF1 polyprotein was generated, and the virus-encoded 3C-like (3CL) proteinase (Pro) mediated cleavage at five dipeptide cleavage sites, 341E/G342, Q705/N706, 870E/G871, 994E/A995, and 1177Q/G1178, that defined the borders of six proteins with the gene order p38.3 (Nterm)-p39.6 (NTPase)-p18.6-p14.3 (VPg)-p19.2 (Pro)-p57.5 (Pol). Bacterially expressed MNV 3CL Pro was sufficient to mediate trans cleavage of the ORF1 polyprotein containing the mutagenized Pro sequence into products identical to those observed during cotranslational processing of the authentic ORF1 polyprotein in vitro and to those observed in MNV-infected cells. Immunoprecipitation and Western blot analysis of proteins produced in virus-infected cells demonstrated efficient cleavage of the proteinase-polymerase precursor. Evidence for additional processing of the Nterm protein in MNV-infected cells by caspase 3 was obtained, and Nterm sequences 118DRPD121 and 128DAMD131 were mapped as caspase 3 cleavage sites by site-directed mutagenesis. The availability of the MNV nonstructural polyprotein cleavage map in concert with a permissive cell culture system should facilitate studies of norovirus replication.
Mitochondrial and Secretory Human Cytomegalovirus UL37 Proteins Traffic into Mitochondrion-Associated Membranes of Human Cells

ABSTRACT The human cytomegalovirus (HCMV) UL37 exon 1 protein (pUL37x1), also known as vMIA, is the predominant UL37 isoform during permissive infection. pUL37x1 is a potent antiapoptotic protein, which prevents cytochrome c release from mitochondria. The UL37x1 NH2-terminal bipartite localization signal, which remains uncleaved, targets UL37 proteins to the endoplasmic reticulum (ER) and then to mitochondria. Based upon our findings, we hypothesized that pUL37x1 traffics from the ER to mitochondria through direct contacts between the two organelles, provided by mitochondrion-associated membranes (MAMs). To facilitate its identification, we cloned and tagged the human phosphatidylserine synthase 1 (huPSS-1) cDNA, whose mouse homologue localizes almost exclusively in the MAM. Using subcellular fractionation of stable HeLa cell transfectants expressing mEGFP-huPSS-1, we found that HCMV pUL37x1 is present in purified microsomes, mitochondria, and MAM fractions. We further examined the trafficking of the full-length UL37 glycoprotein cleavage products, which divergently traffic either through the secretory apparatus or into mitochondria. Surprisingly, pUL37NH2 and gpUL37COOH were both detected in the ER and MAM fraction, even though only pUL37NH2 is preferentially imported into mitochondria but gpUL37COOH is not. To determine the sequences required for MAM importation, we examined pUL37x1 mutants that were partially defective for mitochondrial importation. Deletion mutants of the NH2-terminal UL37x1 mitochondrial localization signal were reduced in trafficking into the MAM, indicating partial overlap of MAM and mitochondrial targeting signals. Taken together, these results suggest that HCMV UL37 proteins traffic from the ER into the MAM, where they are sorted into either the secretory pathway or to mitochondrial importation.
Bayesian peak detection for Pro-TOF MS MALDI data

In this paper, a novel Bayesian peak detection algorithm is proposed for peptide peak detection in high resolution prOTOFtrade MALDI Mass Spectrometry(MS) data. A nonlinear parametric model is proposed for modeling the peptide signals, chemical noise, and thermal noise. A metropolized Gibbs sampling algorithm is derived for Bayesian peak detection. The proposed algorithm is compared with a popular wavelet-based algorithm and the results show a significant improvement in performance on simulated data. The algorithm is finally tested on real MS MALDI data and the results agree with visual inspection very well.
Long-Term Changes in Jump Performance and Maximum Strength in a Cohort of National Collegiate Athletic Association Division I Women's Volleyball Athletes

Abstract Kavanaugh, AA, Mizuguchi, S, Sands, WA, Ramsey, MW, and Stone, MH. Long-term changes in jump performance and maximum strength in a cohort of NCAA division I women's volleyball Athletes. J Strength Cond Res 32(1): 66–75, 2018—The purpose of this investigation was to quantify the magnitude of change in maximal strength and jumping abilities over approximately 1, 2, and 3 years of supervised sport and resistance training in National Collegiate Athletic Association (NCAA) division I women's volleyball athletes. This was an exploratory study on a cohort of women's volleyball athletes (n = 29) split into 3 groups based on the length of the time spent in a supervised resistance training program: group 1 (n = 11): 0.7 ± 0.3 years, group 2 (n = 9): 1.6 ± 0.2 years, and group 3 (n = 9): 2.4 ± 0.6 years. Monitoring tests consisted of standing height (cm), body mass (kg), body fat (%), static jump height (SJH) and countermovement JH (CMJH) with 0-, 11-, and 20-kg loads (cm), and midthigh clean pull isometric peak force (IPF) and allometrically scaled IPF (IPFa) (N·kg−0.67). Increasing trends were observed for all variables from groups 1 to 2 to 3. Statistically greater improvements (p ⩽ 0.05) with moderate to large effect sizes were found between groups 1 and 3 for SJH 0 (19.7%, d = 1.35), SJH 11 (23.8%, d = 1.23), SJH 20 (30.6%, d = 1.20), CMJH 11 (22.6%, d = 1.18), IPF (44.4%, d = 1.22), and IPFa (41.2%, d = 1.32). A combination of traditional resistance training exercises and weightlifting variations at various loads, in addition to volleyball practice, seem to be effective at increasing maximal strength by 44% and vertical JH by 20–30% in NCAA division I women's volleyball athletes after about 2.5 years of training. Furthermore, these characteristics can be improved in the absence of additional plyometric training outside normal volleyball-specific practice.
Decreased Amounts of Cell Wall-Associated Protein A and Fibronectin-Binding Proteins in Staphylococcus aureus sarA Mutants due to Up-Regulation of Extracellular Proteases

ABSTRACT Data have been presented indicating that Staphylococcus aureus cell surface protein can be degraded by extracellular proteases produced by the same bacterium. We have found that insarA mutant cells, which produce high amounts of four major extracellular proteases (staphylococcal serine protease [V8 protease] [SspA], cysteine protease [SspB], aureolysin [metalloprotease] [Aur], and staphopain [Scp]), the levels of cell-bound fibronectin-binding proteins (FnBPs) and protein A were very low compared to those of wild-type cells, in spite of unaltered or increased transcription of the corresponding genes. Cultivation ofsarA mutant cells in the presence of the global protease inhibitor α2-macroglobulin resulted in a 16-fold increase in cell-bound FnBPs, indicating that extracellular proteases were responsible for the decreased amounts of FnBPs in sarAmutant cells. The protease inhibitor E64 had no effect on the level of FnBPs, indicating that cysteine proteases were not involved. Inactivation of either ssp or aur in the prototype S. aureus strain 8325-4 resulted in a threefold increase in the amount of cell-bound FnBPs. Inactivation of the same protease genes in a sarA mutant of 8325-4 resulted in a 10- to 20-fold increase in cell-bound protein A. As the serine protease requires aureolysin to be activated, it can thus be concluded that the serine protease is the most important protease in the release of cell-bound FnBPs and protein A.
Re-engaging students with nature: Using local settings as a context for learning

Students who have difficulty seeing the relevance of classroom curricula often become disengaged from school (Lieberman & Hoody, 1998). High school dropouts cite experiential learning and real world experience as the number one action that would improve their chances of graduating (Azzam, 2007). Using a place-based approach, students can experience integrated, hands-on learning in an outdoor environment that can impact the local community (Sobel, 2005). This study follows students in a locally-developed program. The research specifically looks at the influence of place-based education on their environmental literacy and more broadly, their perceptions of school and learning.
Classes of term rewrite systems with polynomial confluence problems

The confluence property of ground (i.e., variable-free) term rewrite systems (TRS) is well known to be decidable. This was proved independently in Dauchet et al. [1987, 1990] and in Oyamaguchi [1987] using tree automata techniques and ground tree transducer techniques (originated from this problem), yielding EXPTIME decision procedures (PSPACE for strings). Since then, and until last year, the optimality of this bound had been a well-known longstanding open question (see, e.g., RTA-LOOP [2001]). In Comon et al. [2001], we gave the first polynomial-time algorithm for deciding the confluence of ground TRS. Later in Tiwari [2002] this result was extended, using abstract congruent closure techniques, to linear shallow TRS, that is, TRS where no variable occurs twice in the same rule nor at depth greater than one. Here, we give a new and much simpler proof of the latter result.