Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of thermal environment and dietary phosphorus levels in pig gene expression

The purpose of this study was evaluate the effects of temperature and different levels available phosphorus on the expression of ND1, ND2, SDHD, CYTB, COX1, COX2, COX3, ATP5J2 and ATP6 genes encoding electron transport chain proteins in the Longissimus dorsi (LD) muscle of pigs. Two experiments were carried out using 48 higher-lean growth pigs from two different growth phases: phase 1 from 15 to 30 kg and phase 2 from 30 to 60 kg. These experiments were designed as a 2 x 3 (2 temperatures X 3 levels of dietary aP) factorial treatments comprising of 6 treatments and each growth phase. Twenty-four pigs from growth phase 1 (15 to 30 kg) with initial weight of 15 ± 0.41kg, distributed in a completely randomized design with 6 treatments and 6 replications. These pigs were allotted to either thermoneutral (24.5 ± 1.2oC and RH at 76.3 ± 8.5% or heat stress (34.1 ± 0.8oC and RH at 70.1 ± 8.1%) and then allotted to one of the 3 levels of dietary aP (0.107, 0.321 or 0.535%). Twenty-four pigs from growth phase 2 (30 to 60 kg) with initial weight of 30.19 ± 0.30 kg, distributed in a completely randomized design with 6 4 treatments and 6 replications. These pigs were allotted to either thermoneutral ( 21.9 ± 1.4oC and RH at 76.9 ± 5.7%) or heat stress (31.6 ± 0.7oC and RH at 72.8 ± 5.9%) and then allotted to one of the 3 levels of dietary aP (0.116, 0.306 or 0.496%). The expression profiles of 9 genes were analyzed by quantitative real-time PCR. Six genes showed reduce expression (P<0.05) in phase 1 pigs and 8 genes (P<0.05) in phase 2 pigs maintained under heat stress compared to those kept in thermoneutral environment. The lower expression of these genes under high temperatures evidences the effects of heat stress by decreasing oxidative metabolism (oxidative phosphorylation) in order to reduce heat production, which reflecting on the reduction of the daily requirements for aP. Part of this effect is associated with concomitant reduction in voluntary feed intake and another part is suggested to be due to increased production of reactive oxygen species (ROS) in the mitochondria induced by heat stress resulting in downregulation of these genes. In pigs from phase 1, the ND1, ND2, CYTB, COX1, ATP5J2 and ATP6 genes were respectively differentially expressed across aP levels (P<0.05) in the thermoneutral and ND2 gene in the hot environments. In pigs from phase 2, COX3 and ND2 genes were respectively differentially expressed across aP levels (P<0.05) in the thermoneutral and hot environments. These data reveal strong evidence that phosphorus is one of the key factors to regulate oxidative phosphorylation with direct implications on animal performance.
IS APLASTIC ANAEMIA A PKE‐LEUKAEMIC DISORDER?

In this paper we re-examine the relationship between aplastic anaemia (AAJ and leukaemia, and other clonal disorders especially myelodysplasia (MDS) and paroxysmal nocturnal haemoglobinuria (PNH). This has been prompted by recent clinical studies demonstrating a high incidence of the latter occurring as late complications of AA (Tichelli et a / , 1988: de Planque et a/. 1989a). A haemopoietic stem cell defect in AA might be the link between AA and clonal disease, and evidence supporting the importance of an intrinsic stem cell defect in the pathogenesis of AA is reviewed.
MAGIC: A tool for predicting transcription factors and cofactors binding sites in gene sets using ENCODE data

Transcriptomic profiling is an immensly powerful hypothesis generating tool. Whether one is comparing an experimental versus control condition or collecting transcriptomes from cohorts of disease tissue, it is often necessary to determine which transcription factors (TFs) and cofactors drive programs of gene expression in the datasets. Most available tools rely on searching for TF binding motifs near promoters of genes in a gene set. This approach can work well for TFs with extended recognition elements but is less useful for shorter elements and does not work at all for cofactors. The Encyclopedia Of DNA Elements (ENCODE) archives ChIPseq tracks of 169 TFs and cofactors assayed in 91 cells lines. The algorithm presented herein, Multiple Aligned Genomic Integration of ChIP (MAGIC), uses ENCODE ChIPseq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene sets. When compared to a commonly used web resource o-Possum, MAGIC was able to more accurately predict TFs and cofactors that drive gene changes in 3 settings: 1) A cell line expressing or lacking REST, 2) Breast tumors divided along PAM50 designations and 3) Whole brain samples from WT mice or mice lacking CTCF in a particular neuronal subtype. In summary, MAGIC is a standalone application that runs on OSX machines and has a simple interface that produces meaningful predictions of which TFs and cofactors are enriched in a gene set.
Rate and reasons for elective ventilation in patients undergoing intracranial tumour surgery

Abstract Background: Mechanical ventilation (MV) after neurosurgery is often decided by the preoperative neurological status of the patient. However, there is paucity of information regarding factors responsible for continuation of MV in these patients. This study was carried out to identify the indications and risk factors for elective ventilation after intracranial tumour surgery. Materials and Methods: A prospective observational study was carried out on consecutive adult patients who underwent elective craniotomy for tumour excision, and postoperatively required MV. Data on anaesthesia technique, duration of anaesthesia and surgery, blood loss and transfusion and volume of fluids infused were noted. Intraoperative complications like tight brain, massive blood loss, brainstem handling, cranial nerve handling, haemodynamic instability, cardiac arrhythmias, venous air embolism, electrolyte abnormality and hypothermia were also recorded. Statistical analysis was done using Strata 9.0 software. Categorical data was analysed using Chi-square test or Fisher's exact test and continuous data by Student's t-test. Results: A total of 709 patients enrolled for the study over a period of one year out of which 347 patients (48.9%) required continuation of MV during the postoperative period. The mean duration of MV was 29.7 ± 39.7 hrs. The most common causes for postoperative MV were ‘not responding to commands’ (43.2%), and neurosurgeon's advice (41.8%). The mean ICU and hospital stays were 92.2 ± 134.0 hrs and 13.8 ± 16.5 days, respectively. 47.6% of patients who required postoperative MV on neurosurgeon's advice developed complications whereas it was 33.2% for those ventilated other reasons (P < 0.05). Glasgow outcome scale (GOS) at discharge was poor in 12.4%. On multivariate analysis, intraoperative blood transfusion, tracheostomy and duration of ventilation more than 48 hrs were the independent risk factors associated with poor outcome. Conclusions: Although the neurosurgeon's advice for elective ventilation should not be ignored, but prolonged and avoidable MV may exacerbate the postoperative morbidities apart from increasing the cost of treatment. Hence, a complete understanding of intraoperative events, cerebral physiology and various factors influencing it during the perioperative period may not be overemphasised.
Estimating treatment coverage in South African ART clinics based on the time trend of the CD4 count distribution at ART initiation and a dynamical epidemiological model

Estimating treatment coverage in South African ART clinics based on the time trend of the CD4 count distribution at ART initiation and a dynamical epidemiological model Mikateko Cynthia Mazinu Department of Mathematical Sciences, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa. Thesis: MScMath (Mathematics)
Characterizing Journey Time Performance on Urban Metro Systems under Varying Operating Conditions

Automated fare collection (AFC) data provide opportunities for improved measurement of public transport service quality from the passenger perspective. In this paper, AFC data from the London Underground are used to measure service quality through an analysis of journey time performance under regular and incident-affected operating conditions. The analysis involves two parts: (i) parametrically defining the shape of journey time distributions, and (ii) defining three performance metrics based on the moments of the distributions to measure the mean and variance of journey times. The metrics show that mean journey times are longest during the afternoon peak across all lines analyzed, and are more variable during the afternoon and off-peak periods depending on the line. Under incident conditions, mean journey times range from 8% to 39% longer compared with regular conditions, depending on the line. Overall, the main application of this work is that the metrics presented here can be directly applied by operators to quantify customer journey time performance, and can be further extended for industry-wide application to compare performance across metro networks.
Keyword Augmented Nearest Neighbor Search

— Keyword augmented nearest neighbor search operates on spatial database. Traditional nearest neighbor search focus on computing nearest neighbor using keywords . The proposed method investigate into computing nearest neighbor search using keywords by considering features as well as minimum interobjective distance. in a fast manner. It provides a framework for keyword search in spatial databases. It uses the concept of spatial inverted list to store location and keyword and R Tree for storing neighbours of a particular location. R Tree provides fast query performance and comes with algorithm that retrieve nearest neighbour with keywords.
An investigation into the effect of the social environment on the phenotypes of mice lacking Nlgn3 and their wild-type littermates

The main focus of this thesis was to investigate if the social environment may be a factor leading to aberrant behavioural changes in the Nlgn3 knockout mouse, a model of autism spectrum disorder (ASD). Initial observations revealed that mixed genotype housed male Nlgn3 knockout mice and wild-type mice displayed deficits in their social behaviours and anxiety-related behaviours compared to male Nlgn3 knockout mice and wild-type mice in single genotype housed conditions. Selective re-expression of Nlgn3 in parvalbumin expressing cells in transgenic mice rescued their social behaviour and alleviated the phenotypes of their wild-type littermates, thus further indicating that the social behaviour of Nlgn3 knockout mice has a direct and measurable impact on their wild-type littermates’ behaviour. Additionally, the social environment was confirmed to alter the transcriptome profile of the striatum and the hippocampus, as assessed by RNA sequencing. Following this, the question of the sex-specific sensitivity to the social environment was assessed by studying female Nlgn3 knockout mice and their littermates. This revealed that the social environment is a factor influencing the behaviour of female Nlgn3 knockout and wild-type mice. Finally, the potential generalization of the findings to other models for ASD was addressed, by assessing if Neuroligin-3 interacts with other proteins that are known risk factors for ASD. Together, these results demonstrate that Nlgn3 knockout male and female mice show behavioural and physiological changes dependent on the social environment and that this is mediated by parvalbumin-expressing cells. Furthermore, the interaction of Neuroligin-3 with other ASD-related proteins suggest that other mouse models of ASD may also show this sensitivity to the social environment.
Analysis of the pilot survey INKLUGI about aging and disabilities to promote Inclusive Design in industry.

This study is part of the project INKLUGI. The main objective of the project is to create new tools that help to introduce Inclusive Design methods in the industry of the region of Gipuzkoa. To make companies understand the aging of the population as an opportunity for innovation and competitiveness is necessary to create new quantitative tools. The survey about disability and aging is the best way to gather data for a quantitative data base that will feed the future quantitative tools for Inclusive Design. In this study the process followed to carry out the pilot survey INKLUGI is presented. Then, the results obtained from the survey are analysed and discussed in a collaborative workshop with stakeholders. Finally, the contributions of experts from different sectors are explained.
Abnormal Expression of DICER1 Leads to Dysregulation of Inflammatory Effectors in Human Synoviocytes

Dysregulation of multiple microRNAs widely takes place during rheumatoid arthritis (RA) and experimental arthritides. This study is performed to explore the possible mechanism underlying DICER1 deficiency-mediated inflammation in human synoviocytes SW982. Firstly, RNAi of DICER1 led to increased COX2, MMP3, and MMP13 protein production, while DICER1 overexpression could reduce MMP13 expression. Secondly, the increase of IL-8 and decrease of TGF-β1 and TIMP1 were determined in the supernatant derived from DICER1 siRNA-treated cells, while DICER1 overexpression was found capable to reverse this effect. Ingenuity pathway analysis (IPA) software predicted that the Dicer1 deficiency-induced dysregulated cytokines in synoviocytes could possibly lead to the inflammatory disorders in the synovial tissue. Moreover, DICER1 deficiency could also reduce apoptosis, while DICER1 overexpression was found to decrease the proliferation and enhance apoptosis. In addition, DICER1 deficiency could lower the expression of multiple RA-related miRNAs such as miR-155. Meanwhile, DICER1 overexpression could rescue their low expression levels. And then, gain or loss of miR-155 function could regulate the protein levels of MMP3 and MMP13. These results indicated that DICER1 might play its role through regulating its downstream RA-related miRNAs. Our data demonstrated that DICER1 deficiency could cause multiple proinflammatory events in human synoviocytes SW982. This mechanism study might provide the possible target molecule to modify the inflammatory destruction and overproliferation in synoviocytes.
3D Facial Expression Recognition for Defining Users’ Inner Requirements—An Emotional Design Case Study

This study proposes a novel quality function deployment (QFD) design methodology based on customers’ emotions conveyed by facial expressions. The current advances in pattern recognition related to face recognition techniques have fostered the cross-fertilization and pollination between this context and other fields, such as product design and human-computer interaction. In particular, the current technologies for monitoring human emotions have supported the birth of advanced emotional design techniques, whose main focus is to convey users’ emotional feedback into the design of novel products. As quality functional deployment aims at transforming the voice of customers into engineering features of a product, it appears to be an appropriate and promising nest in which to embed users’ emotional feedback with new emotional design methodologies, such as facial expression recognition. This way, the present methodology consists in interviewing the user and acquiring his/her face with a depth camera (allowing three-dimensional (3D) data), clustering the face information into different emotions with a support vector machine classificator, and assigning customers’ needs weights relying on the detected facial expressions. The proposed method has been applied to a case study in the context of agriculture and validated by a consortium. The approach appears sound and capable of collecting the unconscious feedback of the interviewee.
Drug court handbooks suitability for programme participants with low literacy

Objective: The objective of this study was to describe the suitability of adult drug court handbooks for participants with low literacy. Methods: A convenience sample of seven drug court participant handbooks from urban drug courts in three regions of the USA were assessed for reading and literacy suitability for low-literacy learners using the Fry Index Readability Formula and the Suitability Assessment of Materials (SAM). The Fry Index Readability Formula follows an objective approach using a three-step process of counting three random samples of 100-word passages to calculate grade reading level. The SAM uses a 0–2 range scale to assess six distinct factors of written materials to yield a numerical score as superior, adequate or not suitable. Results: All handbooks were written above the reading level for low-literacy learners with scores at the eighth grade reading level or higher. A few handbooks scored adequate ratings in some SAM categories, and only two handbooks scored superior ratings in any one category. Overall SAM scores showed all handbooks were not suitable for low-literacy learners. Conclusion: Findings indicate that drug court participant handbooks from this sample are not written for low-literacy learners. Key recommendations are to develop a drug court handbook appropriate for participants with low literacy, assess drug court participants’ literacy for reading grade level and comprehension and provide multi-modal teaching formats to promote effective learning.
Effectiveness of acupuncture-type interventions to prevent nausea and vomiting during and after cesarean delivery under spinal anesthesia : A systematic review

Effectiveness of acupuncture-type interventions to prevent nausea and vomiting during and after cesarean delivery under spinal anesthesia : A systematic review 오심 및 구토에 대한 계통적 리뷰 논문이다 . 방 제왕절개 척수마취로 인해 침관련 치료에 대한 randomized clinical trials(RCT's)
Advanced vascular access workshop for dialysis nurses: a three-year review

There is increased awareness regarding the benefits of ultrasound for vascular access surveillance and guided cannulation in haemodialysis. However, finding time to train staff whilst working within the clinical setting is challenging. In 2009 a workshop was introduced in Victoria to provide a platform for nursing staff to learn advanced skills in surveillance and cannulation in a safe, supportive environment. The workshop covered topics such as: assessment and cannulation; surgical perspectives in vascular access; radiological perspectives in vascular access; surveillance and monitoring; cannulation competency package; antegrade/ antegrade cannulation; and introduction to ultrasound plus five hours of practical sessions. Feedback from the workshop over the past three years has been positive, and staff have benefited from the both the theoretical and clinical components of the workshop. The success of this workshop highlights the demand for continuing education within the renal workforce.
Epidemiology of Chlamydia trachomatis infection in Finland during 1983–2009

Chlamydia trachomatis epidemic continues at a slowly, albeit steadily increasing rate in the Western world despite health education, easy/user-friendly diagnostic measures, and effective treatment. In Finland, 8,031 and 13,227 C.trachomatis infections were reported in 1995 and 2012, respectively. Over half of the Chlamydia cases were diagnosed among young women, who suffer from the Chlamydia-related complications such as infertility many years after initial infection. The rates of all but first of the following major Chlamydia-related complications: cervical intraepithelial neoplasia, ectopic pregnancy, hospitalized pelvic inflammatory disease, tubal factor infertility have, however, decreased since the 1990s. The aim of this study was to clarify the discordance between the apparently increasing incidence of C. trachomatis and decreasing C.trachomatis IgG antibody rates (seroprevalence). The study material consisted of a random subsample of first trimester serum samples of 7,999 women from the population-based Finnish Maternity Cohort (FMC) registry from 1983 to 2005, and 147,148 women and men with a total of 177,138 C. trachomatis genital infections reported to the Finnish National Infectious Diseases Registry (NIDR) during 1995–2009. Both registries are maintained by the National Institute for Health and Welfare (THL). Serum IgG antibodies were measured by a C.trachomatis major outer membrane proteinspecific peptide enzyme immunoassay (EIA) and the standard micro-immunofluorescence (MIF) method. We found that while C. trachomatis seroprevalences decreased >50% among fertile-aged women the seroconversion rates (seroincidences) were comparable to the NIDR reported rates. The numbers of annual repeated C. trachomatis infection in the NIDR increased until 2009 by 49% in women and 39% in men. In 2009, about 25% of the females and 20% of the males had had an earlier C.trachomatis infection. During the whole follow-up time, 34% of all the repeat diagnoses occurred within 12 months. Most of the first infections were observed among females and males under 25 years of age, but the numbers of repeated chlamydial infections increased up to the age of 30 years. The C. trachomatis serotype distribution changed between the 1980s and 1990s, but the leading 1980 serotypes bounced back by 2005. The numbers of women with multiple serotype infections peaked in the 1990s, and serotypes G and J were temporarily replaced by serotypes E and D. In conclusion, the serological observations fit the polymerase chain reaction (PCR) -based data on C. trachomatis epidemiology. The observed increases in the repeated chlamydial infections among young women and men comply with increasing sexual risk-taking behaviour in Finland. Our observations help to understand the discrepancy between C. trachomatis occurrence and sequelae rates as the overall C. trachomatis infection burden in the population may be decreasing despite the increasing incidence trend.
Modified Modeling and System Stabilization of Shunt Active Power Filter Compensating Loads with μF Capacitance

The interactions between shunt active power filter (APF) and capacitance load tend to result in stability problems and resonance. The conventional model of a shunt APF is not precise enough to reflect this phenomenon. To address it, this paper proposes a modified shunt APF system model to accurately reflect various stability problems. This paper also studies the mechanism of positive feedback resonance brought by capacitance load and proposes a modified hybrid controller to improve the stable margin of the system, making the shunt APF work stably under different working conditions where there are μF capacitors on the demand side. The correctness and validity of the proposed strategy are verified by simulation analysis and prototype experiments.
Production of Magnetic Monopoles via Photon Fusion: Implementation in MadGraph †

If the Dirac magnetic monopoles exist, they can be probed in the collider experiments. Earlier, only the Drell–Yan production mechanism of magnetic monopoles was used to look for magnetic monopoles. However, the photon fusion production mechanism of magnetic monopoles is the dominant production mechanism at the LHC energy. I will discuss the photon fusion production of spin 0, 1/2, and 1 monopoles using the MadGraph event generator. I will also show the kinematic distributions of magnetic monopoles having those three spins. The comparison between the Drell–Yan process and the photon fusion process will also be done.