Miracle-dz/UniFAR-FTUs huggingface dataset:
High Throughput Sequencing and Proteomics to Identify Immunogenic Proteins of a New Pathogen: The Dirty Genome Approach

Background With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. Methods/Principal Findings We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. Conclusions/Significance This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.
Biological Basis for Increased Sensitivity to Radiation Therapy in HPV-Positive Head and Neck Cancers

Although development of head and neck squamous cell carcinomas (HNSCCs) is commonly linked to the consumption of tobacco and alcohol, a link between human papillomavirus (HPV) infection and a subgroup of head and neck cancers has been established. These HPV-positive tumors represent a distinct biological entity with overexpression of viral oncoproteins E6 and E7. It has been shown in several clinical studies that HPV-positive HNSCCs have a more favorable outcome and greater response to radiotherapy. The reason for improved prognosis of HPV-related HNSCC remains speculative, but it could be owned to multiple factors. One hypothesis is that HPV-positive cells are intrinsically more sensitive to standard therapies and thus respond better to treatment. Another possibility is that HPV-positive tumors uniquely express viral proteins that induce an immune response during therapy that helps clear tumors and prevents recurrence. Here, we will review current evidence for the biological basis of increased radiosensitivity in HPV-positive HNSCC.
Heat shock factor-1 modulates p53 activity in the transcriptional response to DNA damage

Here we define an important role for heat shock factor 1 (HSF1) in the cellular response to genotoxic agents. We demonstrate for the first time that HSF1 can complex with nuclear p53 and that both proteins are co-operatively recruited to p53-responsive genes such as p21. Analysis of natural and synthetic cis elements demonstrates that HSF1 can enhance p53-mediated transcription, whilst depletion of HSF1 reduces the expression of p53-responsive transcripts. We find that HSF1 is required for optimal p21 expression and p53-mediated cell-cycle arrest in response to genotoxins while loss of HSF1 attenuates apoptosis in response to these agents. To explain these novel properties of HSF1 we show that HSF1 can complex with DNA damage kinases ATR and Chk1 to effect p53 phosphorylation in response to DNA damage. Our data reveal HSF1 as a key transcriptional regulator in response to genotoxic compounds widely used in the clinical setting, and suggest that HSF1 will contribute to the efficacy of these agents.
Adaptogenic Activity of Lyophilized Hydroethanol Extract of Pandanus odoratissimus in Swiss Albino Mice

Background. The leaves of Pandanus odoratissimus Linn have been widely used in Ayurveda to treat a variety of common and stress related disorders. In the present investigation, hydroethanol extract of leaves of Pandanus odoratissimus Linn (LEPO) were evaluated for antistress activity in normal and stress induced mice. Furthermore, the extract was studied for nootropic (adaptogenic) activity in mice and in vitro antioxidant potential to correlate with its adaptogenic and antistress activity. LEPO (100 and 200 mg/kg p.o) was evaluated against forced swimming endurance stress test, anoxia stress tolerance and immobilization stress and chronic cold resistant stress tests, and biomarkers (serum glucose, Corticosterone, WBC, RBC, and DLC count) to assess the antistress activity in mice. Withania somnifera (WS) (100 mg/kg p.o) was selected as reference standard. The parameters like anoxia stress tolerance time were recorded in anoxia stress and estimation of biochemical marker levels and determination of organs weight were carried out in immobilization stress models. Results. Concomitant treatment with LEPO 200 mg/kg significantly increased in anoxia stress tolerance time. Dose dependent significant reduction in serum glucose, corticosterone, and WBC, RBC, and DLC was observed in immobilisation stress model as compared to stressed group. LEOP 200 mg/kg and WS 100 mg/kg significantly reversed/inhibited the stress induced changes in these parameters. The results from the present study indicate that these values also express that dose dependent significant adaptogenic activity in stressed animals. Conclusion. The present study provides scientific support for the antistress (adaptogenic) and nootropic activities of lyophilized hydroethanol extract of Pandanus odoratissimus Linn and substantiate the traditional claims for the usage of Pandanus in stress induced disorders.
Gender, Feminist and Heterodox Economics: Interconnections and Differences in a Historical Perspective

Despite being interconnected, feminist and gender economics are different. Gender economics represents the application of neoclassical economics to economic issues related to gender, following a neoclassical methodological approach a la Becker that was developed in the New Home Economics. Feminist economics rejects neoclassical economics and it stands for a more pluralistic approach within the broad rubric of economics. This makes feminist economics close to heterodox economics. This paper reveals the history of feminist and gender economics as well as their similarities and differences. It also suggests that amongst heterodox approaches to economics, Austrian economics mostly suits feminist economics: their convergences are focused on the role of cooperation within institutions as well as on the place creativity has in the market and women’s attitude to problem solving.
Wiener's lemma for twisted convolution and Gabor frames

As a consequence, Ca is invertible and bounded on all ? p(Zd) for 1 < p < oo simultaneously. In this article we study several non-commutative generalizations of Wiener's Lemma and their application to Gabor theory. The paper is divided into two parts: the first part (Sections 2 and 3) is devoted to abstract harmonic analysis and extends Wiener's Lemma to twisted convolution. The second part (Section 4) is devoted to the theory of Gabor frames, specifically to the design of dual windows with good time-frequency localization. In particular, we solve a conjecture of Janssen, Feichtinger and one of us [17], [18], [9]. These two topics appear to be completely disjoint, but they are not. The solution of the conjectures about Gabor frames is an unexpected application of methods from non-commutative harmonic analysis to application-oriented mathematics. It turns out that the connection between twisted convolution and the Heisenberg group and the theory of symmetric group algebras are precisely the tools needed to treat the problem motivated by signal analysis. To be more concrete, we formulate some of our main results first and will deal with the details and the technical background later.
Control and Performance in International Joint Ventures

The authors examine the meaning of control in international joint ventures (IJVs) and the relationships of potential means of control in such organizations to the performance satisfaction of the foreign partner. They propose a conceptual model that provides both a traditional ownership-focused internalization perspective on those issues and an integrated approach combining a broader transaction cost interpretation of control with a resource input-based bargaining power model. A set of simultaneous structural equations with endogenous explanatory variables provides multiple possible paths from various resource and power inputs through different means of control to perceived performance satisfaction. In such a model, intermediate variables act both as dependent and independent variables; thus the complex theoretical interactions of the variables are modeled more comprehensively and realistically than in single-equation models.To test the model and compare the theoretical relationships, the authors used data from a survey of managers in Norwegian multinational firms having at least one IJV. For structural equation modeling with latent variables, they used the LISREL VII program that simultaneously fits the measured variables to the latent variables and provides a maximum likelihood solution for the structural equation system. The results clearly reject the traditional internalization approach to IJV governance that relies strictly on ownership share to delineate degree of control. However, relative resource input has a strong relationship to relative bargaining of the parent companies, which then drives equity share, control over specific activities, and perceptions of overall control of the IJV. That result supports a bargaining-power-based model of IJV control. The relatedness of the strategic resources of the parent and the joint venture also drives specific control, implying that although transaction risk is important to governance, governance is provided by specific control rather than ownership level. Perceptions of performance are strongly and positively related to overall control.Those results suggest that specialized control provides both protection and exploitation of key resource inputs and is gained through increased bargaining power. Higher levels of specific control result in a perception of overall control and thereby satisfaction with perceived levels of IJV performance among foreign parent company managers. Interestingly, traditional exogenous determinants of IJV control and performance such as government mandates, cultural similarity, and international experience levels fail to provide significant effects. Rather, the focus is on endogenous aspects of the parent-IJV relationship, suggesting that the key to parent firm satisfaction with an IJV is control over operations that use key strategic inputs from the parent.
Interventional Analgesic Management of Lung Cancer Pain

Lung cancer is one of the four most prevalent cancers worldwide. Comprehensive patient care includes not only adherence to clinical guidelines to control and when possible cure the disease but also appropriate symptom control. Pain is one of the most prevalent symptoms in patients diagnosed with lung cancer; it can arise from local invasion of chest structures or metastatic disease invading bones, nerves, or other anatomical structures potentially painful. Pain can also be a consequence of therapeutic approaches like surgery, chemotherapy, or radiotherapy. Conventional medical management of cancer pain includes prescription of opioids and coadjuvants at doses sufficient to control the symptoms without causing severe drug effects. When an adequate pharmacological medical management fails to provide satisfactory analgesia or when it causes limiting side effects, interventional cancer pain techniques may be considered. Interventional pain management is devoted to the use of invasive techniques such as joint injections, nerve blocks and/or neurolysis, neuromodulation, and cement augmentation techniques to provide diagnosis and treatment of pain syndromes resistant to conventional medical management. Advantages of interventional approaches include better analgesic outcomes without experiencing drug-related side effects and potential for opioid reduction thus avoiding central side effects. This review will describe various pain syndromes frequently described in lung cancer patients and those interventional techniques potentially indicated for those cases.
Causes of Death among Adults in Northern Ethiopia: Evidence from Verbal Autopsy Data in Health and Demographic Surveillance System

Background In countries where registration of vital events is lacking and the proportion of people who die at home without medical care is high, verbal autopsy is used to determine and estimate causes of death. Methods We conducted 723 verbal autopsy interviews of adult (15 years of age and above) deaths from September 2009 to January 2013. Trained physicians interpreted the collected verbal autopsy data, and assigned causes of death according to the international classification of diseases (ICD-10). We did analysis of specific as well as broad causes of death (i.e. non-communicable diseases, communicable diseases and external causes of death) by sex and age using Stata version 11.1. We performed logistic regression to identify socio-demographic predictors using odds ratio with 95% confidence interval and a p-value of 0.05. Findings Tuberculosis, cerebrovascular diseases and accidental falls were leading specific causes of death accounting for 15.9%, 7.3% and 3.9% of all deaths. Two hundred sixty three (36.4% [95% CI: 32.9, 39.9]), 252 (34.9% [95% CI: 31.4, 38.4]) and 89 (12.3% [95% CI: 10.1, 14.9]) deaths were due to non-communicable, communicable diseases, and external causes, respectively. Females had 1.5 times (AOR = 1.53 [95% CI: 1.10, 2.15]) higher odds of dying due to communicable diseases than males. The odds of dying due to external causes were 4 times higher among 15–49 years of age (AOR = 4.02 [95% CI: 2.25, 7.18]) compared to older ages. Males also had 1.7 times (AOR = 1.70 [95% CI: 1.01, 2.85]) higher odds of dying due to external causes than females. Conclusion Tuberculosis, cerebrovascular diseases and accidental falls were the top three causes of death among adults. Efforts to prevent tuberculosis and cerebrovascular diseases related deaths should be improved and safety efforts to reduce accidents should also receive attention.
Cavitation inception of a van der Waals fluid at a sack-wall obstacle

Cavitation in a liquid moving past a constraint is numerically investigated by means of a free-energy lattice Boltzmann simulation based on the van der Waals equation of state. The fluid is streamed past an obstacle, and depending on the pressure drop between inlet and outlet, vapor formation underneath the corner of the sack-wall is observed. The circumstances of cavitation formation are investigated and it is found that the local bulk pressure and mean stress are insufficient to explain the phenomenon. Results obtained in this study strongly suggest that the viscous stress, interfacial contributions to the local pressure, and the Laplace pressure are relevant to the opening of a vapor cavity. This can be described by a generalization of Joseph’s criterion that includes these contributions. A macroscopic investigation measuring mass flow rate behavior and discharge coefficient was also performed. As theoretically predicted, mass flow rate increases linearly with the square root of the pressure drop. Howe.
Analysis on Utilization of Biology Laboratory and School Environment in Biology Learning for Tenth Grade Students of Senior High School in Jepara Regency

The application of 2013 curriculum had teacher to do scientific oriented learning. In fact, scientific oriented learning has not been applied fully in real life. Some obstacle factors are the lack of facility and teacher preparation. This research aims for: (1) analyzing facilities of biology laboratory and school environment, (2) analyzing the utilization of biology laboratory, (3) analyzing the utilization of school environment as learning source of biology subject for first semester of tenth grade students of senior high school. This is a descriptive qualitative research done in seven senior high schools in Jepara Regency. The subjects of this research are tenth grade biology teachers, tenth grade science major students, and vice headmaster (facility division). Data tabulation uses observation, interview, questionnaire, and documentation. Data triangulation uses source and method triangulation. Data analysis uses descriptive. Analysis result provides: 1) the laboratory facility in seven senior high schools in Jepara Regency can be included in “good: category even though it does not fill all the standardization of Permendiknas Number 24, 2007; facility of school environment is in below good category, 2) the utilization of laboratory in biology learning for tenth grade in first semester is in good enough category, 3) the utilization of school environment in biology learning for tenth grade in first semester is in good category. Some factors that influence categories are management of facility, lesson plan made by teachers, teacher understanding about biology material in scientific approach, teachers and students customary to scientific approach, and time allocation.
Constitutively active Notch1 signaling promotes endothelial-mesenchymal transition in a conditional transgenic mouse model

Endothelial-mesenchymal transition (EndoMT) is a process in which endothelial cells lose their cell-type-specific characteristics and gain a mesenchymal cell phenotype. The Notch signaling pathway is crucial in the regulation of EndoMT; however, its roles have not been fully studied in vivo. In a previous study, we reported the generation of transgenic mice with a floxed β-geo/stop signal between a CMV promoter and the constitutively active intracellular domain of Notch1 (IC-Notch1) linked with a human placental alkaline phosphatase (hPLAP) reporter (ZAP-IC-Notch1). In this study, we examined the results of activating IC-Notch1 in endothelial cells. ZAP-IC-Notch1 mice were crossed with Tie2-Cre mice to activate IC-Notch1 expression specifically in endothelial cells. The ZAP-IC-Notch1/Tie2-Cre double transgenic embryos died at E9.5–10.5 with disruption of vasculature and enlargement of myocardium. VE-cadherin expression was decreased and EphrinB2 expression was increased in the heart of these embryos. Mesenchymal cell marker α-smooth muscle actin (SMA) was expressed in IC-Notch1-expressing endothelial cells. In addition, upregulation of Snail, the key effector in mediating EndoMT, was identified in the cardiac cushion of the double transgenic murine embryo heart. The results of the present study demonstrate that constitutively active Notch signaling promotes EndoMT and differentially regulates endothelial/mesenchymal cell markers during cardiac development.
SUBARU MID-INFRARED IMAGING OF THE QUADRUPLE LENSES. II. UNVEILING LENS STRUCTURE OF MG0414+0534 AND Q2237+030

We present mid-infrared imaging at 11.7 μm for the quadruple lens systems, MG0414+0534 and Q2237+030, using the cooled mid-infrared camera and spectrometer attached on the Subaru telescope. MG0414+0534 is characterized by a bright pair of lensed images (A1, A2) and their optical flux ratio A2/A1 deviates significantly from the prediction of a smooth-lens model. Q2237+030 is “the Einstein Cross” being comprised of four lensed images, which are significantly affected by microlensing in a foreground lensing galaxy. Our mid-infrared observations of these lensed images have revealed that the mid-infrared flux ratio for A2/A1 of MG0414+0534 is nearly unity (0.90 ± 0.04). We find that this flux ratio is systematically small, at 4–5σ level, compared with the prediction of a best smooth-lens model (1.09) represented by a singular isothermal ellipsoid and external shear. The smooth-lens model, which also considers the additional lensing effect of the possible faint satellite, object X, still provides a large flux ratio of A2/A1=1.06, thereby suggesting the presence of more substructures that can explain our observational result. In contrast, for Q2237+030, our high signal-to-noise observation indicates that the mid-infrared flux ratios between all the four images of Q2237+030 are virtually consistent with the prediction of a smooth-lens model. Based on the size estimate of the dust torus surrounding the nuclei of these QSOs, we set limits on the mass of a substructure in these lens systems, which can cause anomalies in the flux ratios. For MG0414+0534, since the required mass of a substructure inside its Einstein radius is ≳360 M☉, millilensing by a cold dark matter substructure is most likely. If it is modeled as a singular isothermal sphere, the mass inside a radius of 100 pc is given as ≳1.0 × 105 M☉. For Q2237+030, there is no significant evidence of millilensing, so the reported anomalous flux ratios in shorter wavelengths are entirely caused due to microlensing by stars.
Time Delay in QSO 0957+561 From 1984-1999 Optical Data

Photometric optical data of QSO 0957+561 covering the period 1984-1999 are analyzed to discern between the two values of the time delay (417 and 424 days) mostly accepted in the recent literature. The observations, performed by groups from three different institutions—Princeton University, Harvard-Smithsonian Center for Astrophysics, and Instituto de Astrofísica de Canarias—and including new unpublished 1998-1999 data from the IAC80 Telescope, were obtained in five filters (V, R, I, g, and r). The different light curves have been divided into observational seasons, and two restrictions have been applied to calculate the time delay better: (1) points with a strange photometric behavior have been removed, and (2) data sets without large gaps have been selected. Simulated data were generated to test several numerical methods intended to compute the time delay (ΔτAB). The methods giving the best results—the discrete correlation function, δ2, z-transformed discrete correlation function, and linear interpolation—were then applied to real data. A first analysis of the 23 different time delays derived from each technique shows that ΔτAB must be in the interval 420-424 days. From our statistical study, a most probable value of ΔτAB = 422.6 ± 0.6 days is inferred.
A theoretical typology of border activism: From the streets to the Council

Based on a case study of border struggles within the city of Barcelona since the beginning of the 21st century, this article examines diverse types of border activism. Border activism refers to collective efforts by ordinary people to modify, mitigate or even dismantle a border regime. While several migration and citizenship scholars have analysed migrant protests and struggles, these accounts have been hardly taken into consideration within the field of criminology. My work contributes to this vacuum. Specifically, this article develops a theoretical typology for analysing four different forms of border activism: migrant struggles; de facto citizen struggles; border protests; and institutional border activism. For each form of activism, I consider its framework, the subject position of the political actors involved, the repertoires of contention utilized to achieve change and the impact of the different kinds of local actions for reshaping the border regime and the lives of migrants.