Miracle-dz/UniFAR-FTUs huggingface dataset:
Medical School Librarians Need More Training to Support their Involvement in Evidence Based Medicine Curricula

Objective – To describe the self-perceived role of librarians in developing evidence based medicine (EBM) curricula and identify their current and desired level of training to support these activities. Design – Multi-institutional qualitative study. Setting – Nine medical schools in Canada and the United States of America. Subjects – Nine librarians identified by medical school faculty as central to the provision of EBM training for medical students at their institution. Methods – The researchers designed a semi-structured interview schedule based on a review of the literature and their own experiences as librarians teaching EBM. The topics covered were; librarians’ perceptions of their roles in relation to the curriculum, the training required to enable them to undertake these roles, and their professional development needs. The interviews were conducted by telephone and then audio-recorded and transcribed verbatim. The authors present five main themes; curricular design, curricular deployment, curricular assessment, educational training, and professional development. Profiles were developed for each participant based on the latter two themes and from this information common characteristics were identified. Main Results – The participants described the importance of collaboration with faculty and student bodies when designing a curriculum. Information literacy instruction and specifically literature searching and forming a research question were taught by all of the participants to facilitate curricular deployment. Some of the librarians were involved or partly involved in curricular assessment activities such as formulating exam questions or providing feedback on assignments. Educational training of participants varied from informal observation to formal workshops offered by higher education institutions. All librarians indicated a willingness to partake in professional development focused on teaching and EBM. The subjects’ perceptions of their roles are supported by Dorsch and Perry’s themes of the librarian’s role in curricular design, deployment, and assessment. The educational training received by participants included formal training and experiential and self-directed learning activities. Finally, the librarians identified their professional development needs going forward. The majority of participants indicated that they would like to attend workshops run by universities or the Medical Library Association. Others wanted to invite and host guest speakers at their own institutions. Librarians identified financial restraints and geographic location as barriers to attending professional development events. Conclusion – Librarians can be actively involved in the delivery of EBM instruction in medical schools. However, they require additional educational opportunities to enable them to develop in this role. Online training could be a viable option for self-directed learning to overcome financial and geographic constraints.
Varicella‐Zoster virus ORF9 is an antagonist of the DNA sensor cGAS

Varicella-Zoster virus (VZV) causes chickenpox and shingles. Although infection is associated with severe morbidity in some individuals, molecular mechanisms that determine innate immune responses remain poorly defined. We found that the cGAS/STING DNA sensing pathway was required for type I interferon (IFN) induction during VZV infection and that recognition of VZV by cGAS restricted its replication. Viral gene overexpression screening identified the essential VZV tegument protein ORF9 as a cGAS antagonist. Ectopically and virally expressed ORF9 bound to endogenous cGAS. Confocal microscopy revealed co-localisation of cGAS and ORF9, which reduced the type I IFN response to transfected DNA. ORF9 and cGAS also interacted directly in a cell-free system and phase-separated together with DNA. Furthermore, ORF9 inhibited cGAMP production by cGAS. Taken together, we uncovered the importance of the cGAS/STING DNA sensing pathway for VZV recognition and identified a VZV immune antagonist that directly interferes with DNA sensing via cGAS.
Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogs that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogs using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyper-diverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture exon markers that have been commonly used in fish phylogenetics, despite some being flagged for paralogs, to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes and merged new exon-capture sequence data into an existing data matrix of 1,105 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that loci with known paralogs are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences. These probe sets are a valuable resource for advancing fish phylogenomics because they can be easily extracted from increasingly available whole genome and transcriptome datasets, and also may be integrated with existing PCR-based exon and mitochondrial datasets.
Finding a suitable library size to call variants in RNA-Seq

RNA sequencing allows the study of both gene expression changes and transcribed mutations, providing a highly effective way to gain insight into cancer biology. When planning the sequencing of a large cohort of samples, library size is a fundamental factor affecting both the overall cost and the quality of the results. Here we specifically address how overall library size influences the detection of somatic mutations in RNA-seq data in two acute myeloid leukaemia datasets. We simulated shallower sequencing depths by downsampling 45 acute myeloid leukaemia samples (100 bp PE) that are part of the Leucegene project, which were originally sequenced at high depth. We compared the sensitivity of six methods of recovering validated mutations on the same samples. The methods compared are a combination of three popular callers (MuTect, VarScan, and VarDict) and two filtering strategies. We observed an incremental loss in sensitivity when simulating libraries of 80M, 50M, 40M, 30M and 20M fragments, with the largest loss detected with less than 30M fragments (below 90%, average loss of 7%). The sensitivity in recovering insertions and deletions varied markedly between callers, with VarDict showing the highest sensitivity (60%). Single nucleotide variant sensitivity is relatively consistent across methods, apart from MuTect, whose default filters need adjustment when using RNA-Seq. We also analysed 136 RNA-Seq samples from the TCGA-LAML cohort (50 bp PE) and assessed the change in sensitivity between the initial libraries (average 59M fragments) and after downsampling to 40M fragments. When considering single nucleotide variants in recurrently mutated myeloid genes we found a comparable performance, with a 6% average loss in sensitivity using 40M fragments. Between 30M and 40M 100 bp PE reads are needed to recover 90–95% of the initial variants on recurrently mutated myeloid genes. To extend this result to another cancer type, an exploration of the characteristics of its mutations and gene expression patterns is suggested.
When to change course: timing of treatment change in the management of diabetic macular edema

Diabetes mellitus currently affects at least 1 in 40 persons worldwide, and is expected to affect 1 in 20 people by 2030 (1). Among those affected, approximately one-quarter have diabetic retinopathy (2) and a similar number will go on to develop vision-threatening diabetic macular edema (DME) within 15 years of their initial diagnosis of diabetes (3). Consequently, the growing prevalence of diabetes resulted in the World Health Organization adding diabetic retinopathy to their list of priority eye diseases for which safe and effective treatment is available.
Coupled oscillators for computing: A review and perspective

Coupled oscillators are highly complex dynamical systems, and it is an intriguing concept to use this oscillator dynamics for computation. The idea is not new, but is currently the subject to intense research as part of the quest for “beyond Moore” electronic devices. To a large extent, these efforts are motivated by biological observations: neural systems and mammalian brains, which seem to operate on oscillatory signals. In this paper, we give a survey of oscillator-based computing, with the goal of understanding its promise and limitation for next-generation computing. Our focus will be on the physics of (mostly nanoscale) oscillatory systems and on their characteristics that may enable effective computing.
Multilevel inverter with improved basic unit structure for symmetric and asymmetric source configuration

An improved multilevel inverter (MLI) topology using a new basic unit structure with a reduced number of components is proposed in this study. Its single compact module is made up of two basic units connected to the left and right sides of a packed H-bridge. The topology produces 9-Level output when operated symmetrically and 17-Level output when operated asymmetrically. Identical magnitude of DC sources is used for the symmetrical operation, while non-identical magnitudes in a trinary sequence are used for the asymmetrical operation. The low-frequency modulation scheme is applied for the switching control where the switching angles are pre-calculated. The mathematical formulations for the switching are also considered to reduce the total harmonic distortion (THD) at the output. The proposed topology is also found to be superior in terms of the required number of switches per output level and total blocking voltage compared to conventional and recently reported MLIs. With these merits, real-time installation of the proposed topology will potentially require lesser space and become cheaper. The feasibility of the proposed topology is validated for its 9-Level and 17-Level operations through experimental verification on output characteristics, THD, blocking voltage, power-sharing and efficiency.
Dynamic Ridesharing in Peak Travel Periods

In this paper, we propose and study a variant of the dynamic ridesharing problem with a specific focus on peak hours: Given a set of drivers and a set of rider requests, we aim to match drivers to each rider request by achieving two objectives: maximizing the served rate and minimizing the total additional distance, subject to a series of spatio-temporal constraints. Our problem can be distinguished from existing ridesharing solutions in three aspects: (1) Previous work did not fully explore the impact of peak travel periods where the number of rider requests is much greater than the number of available drivers. (2) Existing ridesharing solutions usually rely on single objective optimization techniques, such as minimizing the total travel cost (either distance or time). (3) When evaluating the overall system performance, the runtime spent on updating drivers’ trip schedules as per newly coming rider requests should be incorporated, while it is unfortunately excluded by most existing solutions. In order to achieve our goal, we propose an underlying index structure on top of a partitioned road network, and compute the lower bounds of the shortest path distance between any two vertices. Using the proposed index together with a set of new pruning rules, we develop an efficient algorithm to dynamically include new riders directly into an existing trip schedule of a driver. In order to respond to new rider requests more effectively, we propose two algorithms that bilaterally match drivers with rider requests. Finally, we perform extensive experiments on a large-scale test collection to validate the effectiveness and efficiency of the proposed methods.
A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis

Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding Bos taurus cattle for increased resistance to bTB is feasible. The utility of such an approach is still unknown for the Bos indicus cattle population. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture in Bos indicus breeds in Cameroon. We conducted a cross-sectional study of slaughter cattle in Cameroon and genotyped a sample of 213 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous studies had found that breed was an important factor in explaining the epidemiology of bTB, with Fulani cattle appearing to be more susceptible than mixed breeds. However, we show that the apparent phenotypic differences in visual appearance between the breeds was not reflected by clear genomic differences. At the genetic level, cattle belonging to different hierarchical genomic clusters differed in their susceptibility to bTB. There was evidence of a genomic association between M. bovis infection status with specific SNPs. We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production.
An Unusual Case of Melioidosis with Psoas Abscess

Melioidosis is an infection caused by a gram negative bacterium . We report a case of FUO which upon investigation revealed muscle abscess and subsequent pus culture revealed melioidosis. This case is reported since melioidosis can often mimic other diseases and in rare instances present with psoas abscess.
İlkokul Dördüncü Sınıf Öğrencilerine Yönelik Özdüzenlemeli Öğrenme Envanteri’nin Geliştirilmesi: Geçerlik ve Güvenirlik Çalışması

Bu arastirmanin amaci dorduncu sinif ogrencilerinin ozduzenlemeli ogrenme duzeylerini belirlemeye yonelik bir olcek gelistirmektir. Gecerlik ve guvenirlik calismalari icin 520 ilkokul dorduncu sinif ogrencisinden veri toplanmistir. Arastirma sonucunda ozduzenlemeli ogrenme envanteri (OOE) ondusunme (12 madde), performans (11 madde) ve ozyansitma (11 madde) olceklerinden olusmustur. Elde edilen olceklerin faktor yukleri . 52 ile . 73 arasinda, madde test korelasyonlarinin ise . 45 ile . 65 arasinda degismektedir. OOE’nun ondusunme, performans ve ozyansitma olceklerinin acikladiklari varyanlar sirasiyla % 40, % 41, % 44 ve ic tutarlik katsayilarinin ise sirasiyla . 86, . 84, . 87 oldugu tespit edilmistir. OOE’nun tum maddeleri icin %27’lik alt ve ust gruplarin olcek puanlari arasinda anlamli fark elde edilmistir. Ayrica 237 kisilik farkli bir orneklem uzerinde gerceklestirilen dogrulayici faktor analizi sonucunda tespit edilen yapinin uyum indeklerinin iyi duzeyde oldugu gorulmustur. Bu sonuclar neticesinde OOE’nun gecerli ve guvenilir bir envanter olarak kullanilabilecegine karar verilmistir.
Sustainable Public Procurement in the Kuwait Public Sector

Sustainable Public Procurement (SPP) is the act of integrating the sustainable development concept into the procurement operations undertaken by the government. The extension of sustainability to public procurement is an emerging area of research; the literature provides little evidence on how to address SPP in general, and specifically in a developing country context. This thesis aims to bridge this gap by investigating the practices of SPP in a developing country such as Kuwait. The primary objective of this doctoral thesis is to assess the current SPP policies and practices in the Kuwait public sector organisations and to identify the main drivers and barriers currently faced by public organisations in their efforts in implementing SPP. This thesis employs quantitative and qualitative research methods supported by the Purchasing Social Responsibility (PSR) model. The data used in the thesis was collected through tender document analysis, semi-structured interviews, and questionnaires distributed among officials in the Kuwait public sector. The results show that some SPP practices are present in the public procurement process. The government is mainly stimulating local industry through intensive use of local products and resources and supporting local suppliers’ business; the findings also convey that health and safety and human rights aspects are the most embedded SPP practices. The results indicate that currently, there is a significant effect of cultural norms and Islam religious beliefs on SPP practices in Kuwait. The finding also shows that financial considerations, whether as the costs of sustainability or its financial benefits, are the most significant factors for implementing SPP in Kuwait public sector organisations. Accordingly, this study has policy implications; I believe that the determinants of sustainability-oriented procurement that resulted from this thesis are useful to public procurement managers, policy makers and SPP scholars, as they could be used as a basis for developing a practical managerial framework, guidelines, and policies to procure more sustainably.
Estimating Electrical Conductivity for Soil Salinity Monitoring Using Various Soil-Water Ratios Depending on Soil Texture

ABSTRACT The electrical conductivity of a saturated paste extract of soil (ECe) is a standard measurement of soil salinity, which may adversely effect the environment and plants. This study aimed to develop a precise linear regression relationship between ECe and electrical conductivity (EC) of different (1:5, 1:2.5, 1:1) soil-water ratios based on soil texture (represented by an index Txw) for the ease and rapid monitoring of soil salinity in an area. Surface (0–20 cm) soil samples (n = 150) from the coastal zone of Bangladesh were analyzed for particle size distribution, and EC by various methods. Entire soil samples were equally divided into two textural groups (finer and coarser) based on Txw values. Necessary statistical treatments were performed to satisfy the conditions of linear regression analysis. Significant correlations (r = −0.44** to −0.56**) were found between Txw and the EC values of various methods within the whole dataset. Derived general (not Txw-assisted, i.e., all data) and specific (Txw-assisted groups) equations followed the model ECe =. Almost all specific equations showed improved coefficient of determinations (mean of all r2 = 0.86; all p < .0001) compared to general ones (mean of all r2 = 0.81; all p < .0001). While validation, corresponding errors (RMSE and/or ME) were found less in the specific equations than the general ones in predicting ECe. Therefore, soil texture (Txw)-based derived equations can preferably be used to predict ECe using other methods for the monitoring of soil salinity in an area.
Combining multifractal analyses of digital mammograms and infrared thermograms to assist in early breast cancer diagnosis

We used a 1D wavelet transform modulus maxima (WTMM) method to analyze the temporal fluctuations of breast skin temperature recorded with an infrared (IR) camera from a panel of patients with breast cancer. This study shows that the multifractal complexity of temperature fluctuations observed in healthy breasts, is lost in the region of the malignant tumor in cancerous breasts. Then, we applied the 2D WTMM method to analyze the spatial fluctuations of breast density in the X-ray mammograms of the same patients. Compared to the correlated roughness fluctuations observed in the healthy areas, some clear loss of correlations is detected in malignant tumor foci. These physiological and architectural changes in the environment of malignant tumors detected in both thermograms and mammograms open new perspectives in computer-aided multifractal methods to assist in early breast cancer diagnosis.
Spectrum of upper gastrointestinal bleed: An experience from Eastern India

Abstract Background/Aims: The etiology of upper gastrointestinal bleed (UGIB) is variable in different geographical regions. Epidemiological data are helpful in knowing the burden of the problem. This study was conducted to know the etiological spectrum, mortality, morbidity, and predictors of outcome in patients with acute UGIB. Materials and Methods: We retrospectively analyzed the data of patients admitted to our hospital between January 2013 and May 2015, with UGIB and noted the clinical presentation, etiology of bleed, and outcome. Results: A total of 337 patients [272 (80.7%) male, 65 (19.3%) female (male:female ratio: 4:1)] of UGIB were included in the study. The mean age of the patients was 55.11 ± 14.8 years (Range - 14–85 years). The most common etiology of UGIB was peptic ulcer (40.05%) followed by varices (33%). Majority of patients were managed medically. Endotherapy was required only in 33% patients. The mean duration of hospital stay was 6.6 ± 5.79 days. Rebleed was seen in 11 (3.2) patients and surgery was required in 6 (1.7%). In hospital, mortality was 2.6%. Age ≥65 years (odds ratio [OR]: 9.5, 95% confidence interval [CI]: 3.108–29.266), serum albumin <3 g/dl (OR: 3.1, 95% CI: 1.049–9.682), and serum creatinine >2 mg/dl (OR: 4.1, 95% CI: 1.068–8.591) were associated with increased mortality. Conclusions: Peptic ulcer disease is still the most common cause of UGIB. Majority of patients can be managed medically. Rebleed rate, need for surgery, and mortality due to UGIB are declining. Elderly age (>65), hypoalbuminemia serum albumin<3g/dl (<3) and renal dysfunction (serum creatinine >2) are important factors associated with increased mortality.
IMMUNOMODULATORY ROLE OF HONEY AND PROPOLIS ON CARBON TETRACHLORIDE (CCl4) INJECTED RATS Original Article

Objective: To evaluate the role of some inflammatory cytokines in hepatic injury induced by carbon tetrachloride (CCl4). Also, the effects of honey bee and propolis extract to modulate the role of these cytokines. Methods: Fifty female Wister rats were divided into five groups, 10 per each group. After 6 w of all treatments, rats were sacrificed, whole blood and serum were collected to determine the number of white blood cells (WBCs), percentage of granulocytes, percentage of lymphocytes and the level of some cytokines such as gamma interferon(INF-γ), tumor necrosis factor(TNF-α) and interleukin-2(IL-2). Results: CCl4 administration resulted in significant increase in the number of WBCs and percentage of granulocytes (P<0.05 and P<0.01 respectively). After treatment with honey and propolis, the number of WBCs was decreased significantly in the case of propolis treatment (P<0.05) compared with CCl4 group. The levels of TNF-α and INF-γ cytokines were significantly decreased (P<0.05) after treatment with honey or propolis compared with CCl4 group. However, there is no significant change in the level of IL-2 after treatment of CCl4 administered rats with honey or propolis. Conclusion: The present study suggested that honey and propolis can improve the immune disorders induced by CCl4 in rats by modulating the levels of inflammatory cytokines, TNF-α, and IFN-γ.