Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Proteomic and Transcriptomic Analysis of Differential Expression of Chicken Lung Tissue in Response to NDV Infection during Heat Stress

Newcastle disease virus (NDV) is a devastating worldwide poultry pathogen with major implications for global food security. In this study, two highly inbred and genetically distinct chicken lines, Fayoumis and Leghorns, were exposed to a lentogenic strain of NDV, while under the effects of heat stress, in order to understand the genetic mechanisms of resistance during high ambient temperatures. Fayoumis, which are relatively more resistant to pathogens than Leghorns, had larger numbers of differentially expressed genes (DEGs) during the early stages of infection when compared to Leghorns and subsequently down-regulated their immune response at the latter stages to return to homeostasis. Leghorns had very few DEGs across all observed time points, with the majority of DEGs involved with metabolic and glucose-related functions. Proteomic analysis corroborates findings made within Leghorns, while also identifying interesting candidate genes missed by expression profiling. Poor correlation between changes observed in the proteomic and transcriptomic datasets highlights the potential importance of integrative approaches to understand the mechanisms of disease response. Overall, this study provides novel insights into global protein and expression profiles of these two genetic lines, and provides potential genetic targets involved with NDV resistance during heat stress in poultry.
Real-time optical coherence tomography observation of retinal tissue damage during laser photocoagulation therapy on ex-vivo porcine samples

Retinal laser photocoagulation represents a widely used treatment for retinal pathologies such as diabetic chorioretinopathy or diabetic edema. For effective treatment, an appropriate choice of the treatment energy dose is crucial to prevent excessive tissue damage caused by over-irradiation of the retina. In this manuscript we investigate simultaneous and time-resolved optical coherence tomography for its applicability to provide feedback to the ophthalmologist about the introduced retinal damage during laser photocoagulation. Time-resolved and volumetric optical coherence tomography data of 96 lesions on ex-vivo porcine samples, set with a 577 nm laser prototype and irradiance of between 300 and 8800 W=cm2 were analyzed. Time-resolved scans were compared to volumetric scans of the lesion and correlated with ophthalmoscopic visibility. Lastly, image parameters extracted from optical coherence tomography Mscans, suitable for lesion classification were identified. Results presented in this work support the hypothesis that simultaneous optical coherence tomography provides valuable information about the extent of retinal tissue damage and may be used to guide retinal laser photocoagulation in the future.
Health Related Quality of Life in Patients with Coronary Heart Disease: Psychological and Socio-Demographical Determinants

Article history: Received: 14 July 2013 Accepted: 23 Aug 2013 Available online: 14 Sep 2013 ZJRMS 2014 Oct; 16(Suppl 1): 40-45 Background: Coronary heart disease is the universal principal cause for decreased quality of life, morbidity, and mortality in adulthood. This study seeks to indicate the psychological and socio-demographical determinants of the health related quality of life in patients with coronary heart disease in Iran. Materials and Methods: In this cross-sectional descriptive design, 205 patients with coronary heart disease among the patients diagnosed with coronary heart disease in Shahid Rajayee heart hospital were selected by compliance sampling and were completed the demographical questionnaire, The WHOQOL-BREF, Tehran-Stockholm marital stress scale (TSMSS) and Mental Health Inventory (MHI-38). Then, data analyzed by stepwise multiple regression analysis by using of the PASW-18. Results: Findings revealed that psychological wellbeing and socio-economic status had significantly positive predictive role on health related quality of life and marital stress, psychological distress, and gender had negatively significant predictive role on health related quality of life (p<0.001). There was no significant role at prediction of health related quality of life in terms of patient's age. Conclusion: It concluded that adverse socio-economic status, female gender, decreased psychological well-being, higher psychological distress and higher marital stress might make patients with coronary heart disease more prone to decreased health related quality of life. Thus, it is important to emphasize the worth of tailored intervention for addressing these issues in therapeutic and rehabilitation agendas. Likewise, the identification and treatment of psycho-social correlates in these patients could be very important. Copyright © 2014 Zahedan University of Medical Sciences. All rights reserved.
Technical Note: Manufacturing of a realistic mouse phantom for dosimetry of radiobiology experiments

PURPOSE The goal of this work was to design a realistic mouse phantom as a useful tool for accurate dosimetry in radiobiology experiments. METHODS A subcutaneous tumor-bearing mouse was scanned in a microCT scanner, its organs manually segmented and contoured. The resulting geometries were converted into a stereolithographic file format (STL) and sent to a multimaterial 3D printer. The phantom was split into two parts to allow for lung excavation and 3D-printed with an acrylic-like material and consisted of the main body (mass density ρ=1.18 g/cm3 ) and bone (ρ=1.20 g/cm3 ). The excavated lungs were filled with polystyrene (ρ=0.32 g/cm3 ). Three cavities were excavated to allow the placement of a 1-mm diameter plastic scintillator dosimeter (PSD) in the brain, the center of the body and a subcutaneous tumor. Additionally, a laser-cut Gafchromic film can be placed in between the two phantom parts for 2D dosimetric evaluation. The expected differences in dose deposition between mouse tissues and the mouse phantom for a 220-kVp beam delivered by the small animal radiation research platform (SARRP) were calculated by Monte Carlo (MC). RESULTS MicroCT scans of the phantom showed excellent material uniformity and confirmed the material densities given by the manufacturer. MC dose calculations revealed that the dose measured by tissue-equivalent dosimeters inserted into the phantom in the brain, abdomen, and subcutaneous tumor would be underestimated by 3-5%, which is deemed to be an acceptable error assuming the proposed 5% accuracy of radiobiological experiments. CONCLUSIONS The low-cost mouse phantom can be easily manufactured and, after a careful dosimetric characterization, may serve as a useful tool for dose verification in a range of radiobiology experiments.
Efficacy and safety of tofacitinib in Japanese patients with rheumatoid arthritis by background methotrexate dose: A post hoc analysis of clinical trial data

Abstract Objectives: Tofacitinib is an oral JAK inhibitor for the treatment of rheumatoid arthritis (RA). We investigated concomitant methotrexate (MTX) dose on tofacitinib efficacy/safety in Japanese RA patients. Methods: This post hoc analysis pooled data from a 3-month phase 2 study (NCT00603512) and a 24-month phase 3 study (NCT00847613). Patients (N= 254) received tofacitinib (low-dose (1 or 3 mg), 5 mg, 10 mg) twice daily (BID) or placebo, with low-dose (>0 to 8 mg/week) or high-dose (>8 mg/week) MTX. Efficacy (ACR20/50/70 and DAS28-4 (ESR)<2.6 response rates; changes from baseline (CFB) in DAS28-4 (ESR) and HAQ-DI) and safety (adverse events (AEs), discontinuations due to AEs, serious AEs, and deaths) were assessed through month 3. Results: At month 3, ACR20/50/70 response rates, mean DAS28-4 (ESR) CFB and HAQ-DI CFB were similar across MTX doses and generally greater for all tofacitinib doses versus placebo. AE rates with low-dose/high-dose MTX were: placebo, 28.6%/52.9%; tofacitinib low-dose, 50.0%/66.7%; 5 mg BID, 56.5%/64.3%; 10 mg BID, 73.8%/67.7%. Conclusion: Tofacitinib efficacy in Japanese RA patients may be unaffected by background MTX dose. AE rates with low-dose versus high-dose MTX were lower with placebo, tofacitinib low-dose or 5 mg BID, but not 10 mg BID, with no apparent differences across system organ class/laboratory parameters.
Boarding out the insane, 1857-1913 : a study of the Scottish system.

The pioneering policy of boarding-out harmless, chronic insane patients in the community was implemented formally by the Scottish Board of Lunacy in 1858, following the passage of the Lunacy (Scotland) Act, 1857. Up to 25% of registered pauper and private patients were boarded-out under the terms of this Act. Despite the innovative nature of the system, the number of patients involved and its marked impact on Scottish lunacy administration, the policy has received little systematic attention this century. This study undertakes, therefore, a detailed assessment of the nature of boarding-out, the demographic and clinical characteristics of patients, the status, role and responsibilities of guardians, and the extent and effect of official supervision. The system was endorsed firmly by the Scottish Commissioners in Lunacy, who advocated its widespread adoption throughout the country. However, despite official encouragement, boarding-out came under sustained attack from certain medical and parish officials and from the general public. Facilitated by extensive recourse to contemporary medical journals, official lunacy reports and parish records, this study assesses the beneficial aspects of the system, and in addition offers a critique of prevailing shortcomings. Physicians from across the world came to see boarding-out in practice. The nature and success of international family care policies, and the extent to which the Scottish system was imitated overseas, therefore, are considered. Boarding-out continued to be utilised in the 20th century, albeit with a gradual transformation in its nature. The changing nature of boarding-out is examined, and its gradual decline, and replacement by the less closely organised policy of community care explored, thereby enabling tentative analogies to be drawn between the two systems.
Phycoremediation of Municipal Wastewater by the Cold‐Adapted Microalga Monoraphidium sp. Dek19

Present municipal wastewater treatment technologies often require substantial energy inputs, and fail to completely remove nitrate and phosphate before discharging effluent. In contrast, using the cold‐adapted oleaginous microalga Monoraphidium sp. Dek 19 decreased levels of both these polluting ions to 0 mg/dL. Concurrent biomass production was greater at 10 °C than at 22 °C, showing that phycoremediation occurred at low temperatures previously thought to be unsuitable for algal‐based treatment. Algal growth with uptake of nitrate and phosphate required only short bursts of aeration to suspend cells and maintain CO2 supply for photosynthesis. To save energy, culture aeration for 1 hour, 4 times per day, including during the dark cycle, yielded cell productivity and phycoremediation nearly equivalent to using 24‐hour aeration. The authors conclude that Monoraphidium sp. Dek19 algae represent an economical effluent treatment at cool temperatures found in the high proportion of water resource recovery facilities in geographical areas experiencing cold winters.
Seminal immunologic discoveries with direct clinical implications: The 2018 Nobel Prize in Physiology or Medicine honours discoveries in cancer immunotherapy

The Nobel Assembly at Karolinska Institutet has awarded the 2018 Nobel Prize in Physiology or Medicine to two immunologists, James P. Allison and Tasuku Honjo, for their discoveries of cancer therapy by inhibition of negative immune regulation. The prize is a testimony to basic research, which in the minds of great scientists has driven clinical translation with unusual speed. In the 1990s, at the University of California, Berkeley, Allison studied the molecule CTLA‐4 on T cells, a key molecule that functions as a brake on T cells. Having developed an antibody that could block the function of CTLA‐4, Allison set out to investigate if anti‐CTLA‐4 antibodies could unleash restrained T cells, resulting in an attack on cancer cells. In a first set of experiment, mice with cancer were cured by treatment with the antibody. Despite limited interest from the pharmaceutical industry, Allison continued his efforts to develop a therapy for humans. Promising results soon emerged, and in 2010, an important clinical study showed striking effects in patients with advanced melanoma. In 1992, a few years before Allison's discovery, Tasuku Honjo had identified PD‐1, another protein expressed on the surface of T cells. Determined to unravel its role, he explored its function and showed that PD‐1, similar to CTLA‐4, also functioned as a T cell brake. In animal experiments, PD‐1 blockade emerged as a promising strategy in the fight against tumors, paving the way for utilizing PD‐1 as a target in the treatment of cancer patients. Clinical development ensued, and a clear efficacy in patients with different types of cancer following PD‐1 blockade has now been shown. A remarkable feature of checkpoint blockade is its capacity to induce long‐term remission, and maybe even long‐term cure, in patients with metastatic cancer. The clinical development is promising for patients with many types of cancers that are difficult to treat, including melanoma, lung cancer and kidney cancer. A major challenge is to understand heterogeneity in patient responses, but already now it is clear that checkpoint therapy, utilizing anti‐ CTLA‐4 and/or anti‐PD‐1 antibodies, has revolutionized cancer immunotherapy and the way we view how cancer can be managed.
Developing the Guided Learner Journey

The University of Hertfordshire was one of the first UK universities to embrace the use of a Virtual Learning Environment (VLE) and embed it as part of our learning strategy to personalise and enhance the student experience. Our in-house built platform, Studynet, which has been in continuous use and ongoing development since 2001, has facilitated a continuum of student engagement from blended approaches to studying via online or distance learning modes. In 2014 we embarked on a two year, in-depth consultation process with students and staff to identify the vision for our future online environment. Through the process we co-developed a set of pedagogic principles and aspirations for our new VLE which resulted in our vision of a ‘Guided Learner Journey’ (GLJ). To enable our vision we purchased Canvas (a virtual learning environment) and Talis (a reading management software) and through our close working relationship, and the innovative approach of Canvas, we have embedded the softwares within Studynet to enable the implementation of the GLJ. In our presentation we will share our consultation and prototyping process as well as well as training programme we have developed to ensure the smooth implementation of our vision. Introduction The University of Hertfordshire is a post-92 institution with 24,500 students (including over 3500 international students) and over 2000 staff. We were one of the first universities in the UK to embrace the use of a Virtual Learning Environment (VLE) and embed it as part of our learning and teaching strategy to personalise and enhance the student experience. Our inhouse built platform, Studynet, has been in continuous use and development since 2001, and has facilitated a continuum of student engagement from blended approaches to online distance learning. Studynet performs to a very high standard and is very much embedded into the University culture and working practices. Recognising limitations of the programming software on which Studynet was developed and the need to consider the requirements of an online learning environment fit for the future (Burnes, 2004) we embarked on a large scale change management process. Kanter et al’s (1992) ‘10 commandments for executing change’ identify the importance of communicating, involving people and being honest so in 2014 we embarked on an extensive and University wide consultation process. Through the consultation we aimed to articulate a shared vision through empowering individuals from all parts of the Institution (Kotter, 1996). As Luecke (2003), advocates within the ‘Seven Steps to Change’ “Start change at the periphery, then let it spread to other units without pushing it from the top” which was a very important approach for us. Our consultation processes included: • discussion forums with staff from all 10 academic Schools • student focus groups including students from all Schools and all levels of study
Audiovisual Lexical Retrieval Deficits Following Left Hemisphere Stroke

Binding sensory features of multiple modalities of what we hear and see allows formation of a coherent percept to access semantics. Previous work on object naming has focused on visual confrontation naming with limited research in nonverbal auditory or multisensory processing. To investigate neural substrates and sensory effects of lexical retrieval, we evaluated healthy adults (n = 118) and left hemisphere stroke patients (LHD, n = 42) in naming manipulable objects across auditory (sound), visual (picture), and multisensory (audiovisual) conditions. LHD patients were divided into cortical, cortical–subcortical, or subcortical lesions (CO, CO–SC, SC), and specific lesion location investigated in a predictive model. Subjects produced lower accuracy in auditory naming relative to other conditions. Controls demonstrated greater naming accuracy and faster reaction times across all conditions compared to LHD patients. Naming across conditions was most severely impaired in CO patients. Both auditory and visual naming accuracy were impacted by temporal lobe involvement, although auditory naming was sensitive to lesions extending subcortically. Only controls demonstrated significant improvement over visual naming with the addition of auditory cues (i.e., multisensory condition). Results support overlapping neural networks for visual and auditory modalities related to semantic integration in lexical retrieval and temporal lobe involvement, while multisensory integration was impacted by both occipital and temporal lobe lesion involvement. The findings support modality specificity in naming and suggest that auditory naming is mediated by a distributed cortical–subcortical network overlapping with networks mediating spatiotemporal aspects of skilled movements producing sound.
Knowledge about prevention, risk factors and treatment in women with diagnosed breast cancer. Whether the disease affects their healthy behaviour?

Objective. The assessment of knowledge about prevention and risk factors of women with diagnosed breast cancer. Material and methods. The study involved 100 women aged from 28 to 82 years (median 56.2 years) who were treated at the Oncology Center in Bydgoszcz in 2014 for breast cancer. Author’s original questionnaire containing questions on knowledge about breast cancer as well as environmental and demographic data was used in this research. Results. Self-examination of a breast was made by 83% of women, 85% of women benefited from invitations for mammography. 56% of women knew how often mammography should be repeated but only 28% knew at what age it should be started. Tumor in a breast (20.5%) and “pulling” nipples (14.4%) were the most frequently reported symptoms of a cancer. In terms of risk factors, genetics (32.2%) and unhealthy lifestyle (16.3%) were the factors pointed by women most often. Every third women indicated only one factor while every four indicated three factors. 69% of the respondents increased their knowledge after falling ill, from the Internet (20.5%) as well as from information leaflets and brochures (16.6%). Women’s knowledge about breast cancer was at the edge of low and average levels and the average value was 11.7 points. More knowledge had women with higher education 12.95 points, single 12.9 and young women 12.3. Conclusions. The knowledge about the disease among women with diagnosed breast cancer was unsatisfactory and did not depend on age, marital status, place of residence, type of work but on education level only. Older and uneducated women had less knowledge, particularly about factors increasing the risk of developing the disease. The Internet, information leaflets and brochures were the primary source of knowledge about the disease, not a doctor or a nurse. Women with breast cancer were aware of the importance of preventive tests. They declared that they can perform self-examination. The most frequently reported symptoms of cancer are tumor and “pulling” nipples.
Bayesian Networks: An Introduction

Bayesian Networks: An Introduction provides a self-contained introduction to the theory and applications of Bayesian networks, a topic of interest and importance for statisticians, computer scientists and those involved in modelling complex data sets. The material has been extensively tested in classroom teaching and assumes a basic knowledge of probability, statistics and mathematics. All notions are carefully explained and feature exercises throughout. Features include: An introduction to Dirichlet Distribution, Exponential Families and their applications. A detailed description of learning algorithms and Conditional Gaussian Distributions using Junction Tree methods. A discussion of Pearl's intervention calculus, with an introduction to the notion of see and do conditioning. All concepts are clearly defined and illustrated with examples and exercises. Solutions are provided online. This book will prove a valuable resource for postgraduate students of statistics, computer engineering, mathematics, data mining, artificial intelligence, and biology. Researchers and users of comparable modelling or statistical techniques such as neural networks will also find this book of interest.
Citation analysis as an unobtrusive method for journal collection evaluation using psychology studen

A cemetery monument including a base and a main body section extending upwardly from the base; the body section including an outer shell formed of a plurality of textured corrosion-resistant metal panels, the edges of which are affixed to each other to form a substantially enclosed chamber, the body section having at least one opening in the face portion thereof, the face portion having peripheral flanges around the opening therein extending into the interior of the body section, a text display member disposed within the opening with surfaces thereof adjacent to the perpheral flanges, means for securing the text display member to the peripheral flanges including a plurality of pins disposed through openings in the peripheral flanges and extending into the test display member, and the chamber of the body section being substantially filled with concrete.
The prevention, treatment, and outcomes of Staphylococcus aureus infections

ii ACKNOWLEDGMENTS I want to thank my thesis committee members Dr. and Dr. Loreen Herwaldt for mentoring me during my graduate education. I want to acknowledge the many people who assisted with these projects. I thank the VINCI data and creating a manageable dataset for my thesis project. I specifically want to thank for assisting me with the laboratory projects and for the encouragement and support throughout this entire process. These projects would have not been possible without the financial support provided by a Grant from the Centers for Disease Control and Prevention (5R18CI000583), a Young Investigator Award from Pfizer #WS79560E, and Dr. Marin Schweizer's VA HSR&D career development award.
YÜKSEK ÖĞRETİMDE DEĞİŞİM: GLOBAL TRENDLER ve YENİ PARADİGMALAR

Degisim caginda yasiyoruz. Iktisadi, siyasi, sosyal, demografik, teknolojik vs degisimler yeni dunya duzenini olusturuyor. Globallesme, bilgi devrimi, bilimsel gelismeler, bilgi ve iletisim teknolojileri, e-ticaret, e-devlet gozlemledigimiz degisimlerin baslicalarini olusturuyor. Bu buyuk transformasyon yuksek ogretimde de degisimi gundeme getiriyor. Bu calismanin amaci yuksek ogretimdeki degism trendlerini ve yeni paradigmalari incelemektir.